fix: replace shell-based context updates with marker-based upsert (#2259)

* Replace shell-based context updates with marker-based upsert

Replace ~3500 lines of bash/PowerShell agent context update scripts
with a Python-based approach using <!-- SPECKIT START/END --> markers.

IntegrationBase now manages the agent context file directly:
- upsert_context_section(): creates or updates the marked section at
  init/install/switch time with a directive to read the current plan
- remove_context_section(): removes the section at uninstall, deleting
  the file only if it becomes empty
- __CONTEXT_FILE__ placeholder in command templates is resolved per
  integration so the plan command references the correct agent file
- context_file is persisted in init-options.json for extension access

The plan command template instructs the LLM to update the plan
reference between the markers in the agent context file.

Removed:
- scripts/bash/update-agent-context.sh (857 lines)
- scripts/powershell/update-agent-context.ps1 (515 lines)
- 56 integration wrapper scripts (update-context.sh/.ps1)
- templates/agent-file-template.md
- agent_scripts frontmatter key and {AGENT_SCRIPT} replacement logic
- update-context reference from integration.json
- tests/test_cursor_frontmatter.py (tested deleted scripts)

Added:
- upsert/remove context section methods on IntegrationBase
- __CONTEXT_FILE__ placeholder support in process_template()
- context_file field in init-options.json (init/switch/uninstall)
- Per-integration tests: context file correctness, plan reference,
  init-options persistence (78 new context_file tests)
- End-to-end CLI validation across all 28 integrations

* fix: search for end marker after start marker in context section methods

Address Copilot review: content.find(CONTEXT_MARKER_END) searched from
the start of the file rather than after the located start marker. If
the file contained a stray end marker before the start marker, the
wrong slice could be replaced.

Now both upsert_context_section() and remove_context_section() pass
start_idx as the second argument to find() and validate end_idx >
start_idx before performing the replacement.

* fix: address Copilot review feedback on context section handling

1. Fix grammar in _build_context_section() directive text — add commas
   for a complete sentence.

2. Resolve __CONTEXT_FILE__ in resolve_skill_placeholders() — skills
   generated via extensions/presets for codex/kimi now replace the
   placeholder using the context_file value from init-options.json.

3. Handle Cursor .mdc frontmatter — when creating a new .mdc context
   file, prepend alwaysApply: true YAML frontmatter so Cursor
   auto-loads the rules.

4. Fix empty-file leading newline — when the context file exists but
   is empty, write the section directly instead of prepending a blank
   line.

* fix: address second round of Copilot review feedback

1. Ensure .mdc frontmatter on existing files — upsert_context_section()
   now checks for missing YAML frontmatter on .mdc files during updates
   (not just creation), so pre-existing Cursor files get alwaysApply.

2. Guard against context_file=None — use 'or ""' instead of a default
   arg so explicit null values in init-options.json don't cause a
   TypeError in str.replace().

3. Clean up .mdc files on removal — remove_context_section() treats
   files containing only the Speckit-generated frontmatter block as
   empty, deleting them rather than leaving orphaned frontmatter.

* fix: address third round of Copilot review feedback

1. CRLF-safe .mdc frontmatter check — use lstrip().startswith('---')
   instead of startswith('---\n') so CRLF files don't get duplicate
   frontmatter.

2. CRLF-safe .mdc removal check — normalize line endings before
   comparing against the sentinel frontmatter string.

3. Call remove_context_section() during integration_uninstall() — the
   manifest-only uninstall was leaving the managed SPECKIT markers
   behind in the agent context file.

4. Fix stale docstring — remove 'agent_scripts' mention from
   test_lean_commands_have_no_scripts().

* fix: address fourth round of Copilot review feedback

1. Remove unused script_type parameter from _write_integration_json()
   and all 3 call sites — the parameter was no longer referenced after
   the update-context script removal.

2. Fix _build_context_section() docstring — correct example path from
   '.specify/plans/plan.md' to 'specs/<feature>/plan.md'.

3. Improve .mdc frontmatter-only detection in remove_context_section()
   — use regex to match any YAML frontmatter block (not just the exact
   Speckit-generated one), so .mdc files with additional frontmatter
   keys are also cleaned up when no body content remains.

* fix: handle corrupted markers and parse .mdc frontmatter robustly

1. Handle partial/corrupted markers in upsert_context_section() —
   if only the START marker exists (no END), replace from START
   through EOF. If only the END marker exists, replace from BOF
   through END. This keeps upsert idempotent even when a user
   accidentally deletes one marker.

2. Parse .mdc YAML frontmatter properly — new _ensure_mdc_frontmatter()
   helper parses existing frontmatter and ensures alwaysApply: true is
   set, rather than just checking for the --- delimiter. Handles
   missing frontmatter, existing frontmatter without alwaysApply, and
   already-correct frontmatter.

* fix: preserve .mdc frontmatter, add tests, clean up on switch

1. Rewrite _ensure_mdc_frontmatter() with regex — preserves comments,
   formatting, and custom keys in existing frontmatter instead of
   destructively re-serializing via yaml.safe_dump(). Inserts or
   fixes alwaysApply: true in place.

2. Add 6 focused .mdc frontmatter tests to cursor-agent test file:
   new file creation, missing frontmatter, preserved custom keys,
   wrong alwaysApply value, idempotent upserts, removal cleanup.

3. Call remove_context_section() during integration switch Phase 1 —
   prevents stale SPECKIT markers from being left in the old
   integration's context file. Also clear context_file from
   init-options during the metadata reset.

* fix: remove unused MDC_FRONTMATTER, preserve inline comments, normalize bare CR

1. Remove unused MDC_FRONTMATTER class variable — dead code after
   _ensure_mdc_frontmatter() was rewritten with regex.

2. Preserve inline comments when fixing alwaysApply — the regex
   substitution now captures trailing '# comment' text and keeps it.

3. Normalize bare CR in upsert_context_section() — match the
   behavior of remove_context_section() which already normalizes
   both CRLF and bare CR.

4. Clarify .mdc removal comment — 'treat frontmatter-only as empty'
   instead of misleading 'strip frontmatter'.

* fix: handle corrupted markers in remove, CRLF-safe end-marker consumption

1. Handle corrupted markers in remove_context_section() — mirror
   upsert's behavior: start-only removes start→EOF, end-only removes
   BOF→end. Previously bailed out leaving partial markers behind.

2. CRLF-safe end-marker consumption — both upsert and remove now
   handle \r\n after the end marker, not just \n. Prevents extra
   blank lines at replacement boundaries in CRLF files.

3. Clarify path rule in plan template — distinguish filesystem
   operations (absolute paths) from documentation/agent context
   references (project-relative paths).

* fix: only remove context section when both markers are well-ordered

remove_context_section() previously treated mismatched markers as
corruption and aggressively removed from BOF→end-marker or
start-marker→EOF, which could delete user-authored content if only
one marker remained. Now it only removes when both START and END
markers exist and are properly ordered, returning False otherwise.

pyproject.toml

@@ -28,7 +28,6 @@ packages = ["src/specify_cli"]
 [tool.hatch.build.targets.wheel.force-include]
 # Bundle core assets so `specify init` works without network access (air-gapped / enterprise)
 # Page templates (exclude commands/ — bundled separately below to avoid duplication)
-"templates/agent-file-template.md" = "specify_cli/core_pack/templates/agent-file-template.md"
 "templates/checklist-template.md" = "specify_cli/core_pack/templates/checklist-template.md"
 "templates/constitution-template.md" = "specify_cli/core_pack/templates/constitution-template.md"
 "templates/plan-template.md" = "specify_cli/core_pack/templates/plan-template.md"

scripts/bash/update-agent-context.sh

@@ -1,857 +0,0 @@
-#!/usr/bin/env bash
-
-# Update agent context files with information from plan.md
-#
-# This script maintains AI agent context files by parsing feature specifications 
-# and updating agent-specific configuration files with project information.
-#
-# MAIN FUNCTIONS:
-# 1. Environment Validation
-#    - Verifies git repository structure and branch information
-#    - Checks for required plan.md files and templates
-#    - Validates file permissions and accessibility
-#
-# 2. Plan Data Extraction
-#    - Parses plan.md files to extract project metadata
-#    - Identifies language/version, frameworks, databases, and project types
-#    - Handles missing or incomplete specification data gracefully
-#
-# 3. Agent File Management
-#    - Creates new agent context files from templates when needed
-#    - Updates existing agent files with new project information
-#    - Preserves manual additions and custom configurations
-#    - Supports multiple AI agent formats and directory structures
-#
-# 4. Content Generation
-#    - Generates language-specific build/test commands
-#    - Creates appropriate project directory structures
-#    - Updates technology stacks and recent changes sections
-#    - Maintains consistent formatting and timestamps
-#
-# 5. Multi-Agent Support
-#    - Handles agent-specific file paths and naming conventions
-#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Junie, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Tabnine CLI, Kiro CLI, Mistral Vibe, Kimi Code, Pi Coding Agent, iFlow CLI, Forge, Goose, Antigravity or Generic
-#    - Can update single agents or all existing agent files
-#    - Creates default Claude file if no agent files exist
-#
-# Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic
-# Leave empty to update all existing agent files
-
-set -e
-
-# Enable strict error handling
-set -u
-set -o pipefail
-
-#==============================================================================
-# Configuration and Global Variables
-#==============================================================================
-
-# Get script directory and load common functions
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$SCRIPT_DIR/common.sh"
-
-# Get all paths and variables from common functions
-_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
-eval "$_paths_output"
-unset _paths_output
-
-NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
-AGENT_TYPE="${1:-}"
-
-# Agent-specific file paths  
-CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
-GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/copilot-instructions.md"
-CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
-QWEN_FILE="$REPO_ROOT/QWEN.md"
-AGENTS_FILE="$REPO_ROOT/AGENTS.md"
-WINDSURF_FILE="$REPO_ROOT/.windsurf/rules/specify-rules.md"
-JUNIE_FILE="$REPO_ROOT/.junie/AGENTS.md"
-KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
-AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
-ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
-CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
-QODER_FILE="$REPO_ROOT/QODER.md"
-# Amp, Kiro CLI, IBM Bob, Pi, Forge, and Goose all share AGENTS.md — use AGENTS_FILE to avoid
-# updating the same file multiple times.
-AMP_FILE="$AGENTS_FILE"
-SHAI_FILE="$REPO_ROOT/SHAI.md"
-TABNINE_FILE="$REPO_ROOT/TABNINE.md"
-KIRO_FILE="$AGENTS_FILE"
-AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
-BOB_FILE="$AGENTS_FILE"
-VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
-KIMI_FILE="$REPO_ROOT/KIMI.md"
-TRAE_FILE="$REPO_ROOT/.trae/rules/project_rules.md"
-IFLOW_FILE="$REPO_ROOT/IFLOW.md"
-FORGE_FILE="$AGENTS_FILE"
-
-# Template file
-TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
-
-# Global variables for parsed plan data
-NEW_LANG=""
-NEW_FRAMEWORK=""
-NEW_DB=""
-NEW_PROJECT_TYPE=""
-
-#==============================================================================
-# Utility Functions
-#==============================================================================
-
-log_info() {
-    echo "INFO: $1"
-}
-
-log_success() {
-    echo "✓ $1"
-}
-
-log_error() {
-    echo "ERROR: $1" >&2
-}
-
-log_warning() {
-    echo "WARNING: $1" >&2
-}
-
-# Track temporary files for cleanup on interrupt
-_CLEANUP_FILES=()
-
-# Cleanup function for temporary files
-cleanup() {
-    local exit_code=$?
-    # Disarm traps to prevent re-entrant loop
-    trap - EXIT INT TERM
-    if [ ${#_CLEANUP_FILES[@]} -gt 0 ]; then
-        for f in "${_CLEANUP_FILES[@]}"; do
-            rm -f "$f" "$f.bak" "$f.tmp"
-        done
-    fi
-    exit $exit_code
-}
-
-# Set up cleanup trap
-trap cleanup EXIT INT TERM
-
-#==============================================================================
-# Validation Functions
-#==============================================================================
-
-validate_environment() {
-    # Check if we have a current branch/feature (git or non-git)
-    if [[ -z "$CURRENT_BRANCH" ]]; then
-        log_error "Unable to determine current feature"
-        if [[ "$HAS_GIT" == "true" ]]; then
-            log_info "Make sure you're on a feature branch"
-        else
-            log_info "Set SPECIFY_FEATURE environment variable or create a feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if plan.md exists
-    if [[ ! -f "$NEW_PLAN" ]]; then
-        log_error "No plan.md found at $NEW_PLAN"
-        log_info "Make sure you're working on a feature with a corresponding spec directory"
-        if [[ "$HAS_GIT" != "true" ]]; then
-            log_info "Use: export SPECIFY_FEATURE=your-feature-name or create a new feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if template exists (needed for new files)
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_warning "Template file not found at $TEMPLATE_FILE"
-        log_warning "Creating new agent files will fail"
-    fi
-}
-
-#==============================================================================
-# Plan Parsing Functions
-#==============================================================================
-
-extract_plan_field() {
-    local field_pattern="$1"
-    local plan_file="$2"
-    
-    grep "^\*\*${field_pattern}\*\*: " "$plan_file" 2>/dev/null | \
-        head -1 | \
-        sed "s|^\*\*${field_pattern}\*\*: ||" | \
-        sed 's/^[ \t]*//;s/[ \t]*$//' | \
-        grep -v "NEEDS CLARIFICATION" | \
-        grep -v "^N/A$" || echo ""
-}
-
-parse_plan_data() {
-    local plan_file="$1"
-    
-    if [[ ! -f "$plan_file" ]]; then
-        log_error "Plan file not found: $plan_file"
-        return 1
-    fi
-    
-    if [[ ! -r "$plan_file" ]]; then
-        log_error "Plan file is not readable: $plan_file"
-        return 1
-    fi
-    
-    log_info "Parsing plan data from $plan_file"
-    
-    NEW_LANG=$(extract_plan_field "Language/Version" "$plan_file")
-    NEW_FRAMEWORK=$(extract_plan_field "Primary Dependencies" "$plan_file")
-    NEW_DB=$(extract_plan_field "Storage" "$plan_file")
-    NEW_PROJECT_TYPE=$(extract_plan_field "Project Type" "$plan_file")
-    
-    # Log what we found
-    if [[ -n "$NEW_LANG" ]]; then
-        log_info "Found language: $NEW_LANG"
-    else
-        log_warning "No language information found in plan"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        log_info "Found framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        log_info "Found database: $NEW_DB"
-    fi
-    
-    if [[ -n "$NEW_PROJECT_TYPE" ]]; then
-        log_info "Found project type: $NEW_PROJECT_TYPE"
-    fi
-}
-
-format_technology_stack() {
-    local lang="$1"
-    local framework="$2"
-    local parts=()
-    
-    # Add non-empty parts
-    [[ -n "$lang" && "$lang" != "NEEDS CLARIFICATION" ]] && parts+=("$lang")
-    [[ -n "$framework" && "$framework" != "NEEDS CLARIFICATION" && "$framework" != "N/A" ]] && parts+=("$framework")
-    
-    # Join with proper formatting
-    if [[ ${#parts[@]} -eq 0 ]]; then
-        echo ""
-    elif [[ ${#parts[@]} -eq 1 ]]; then
-        echo "${parts[0]}"
-    else
-        # Join multiple parts with " + "
-        local result="${parts[0]}"
-        for ((i=1; i<${#parts[@]}; i++)); do
-            result="$result + ${parts[i]}"
-        done
-        echo "$result"
-    fi
-}
-
-#==============================================================================
-# Template and Content Generation Functions
-#==============================================================================
-
-get_project_structure() {
-    local project_type="$1"
-    
-    if [[ "$project_type" == *"web"* ]]; then
-        echo "backend/\\nfrontend/\\ntests/"
-    else
-        echo "src/\\ntests/"
-    fi
-}
-
-get_commands_for_language() {
-    local lang="$1"
-    
-    case "$lang" in
-        *"Python"*)
-            echo "cd src && pytest && ruff check ."
-            ;;
-        *"Rust"*)
-            echo "cargo test && cargo clippy"
-            ;;
-        *"JavaScript"*|*"TypeScript"*)
-            echo "npm test && npm run lint"
-            ;;
-        *)
-            echo "# Add commands for $lang"
-            ;;
-    esac
-}
-
-get_language_conventions() {
-    local lang="$1"
-    echo "$lang: Follow standard conventions"
-}
-
-# Escape sed replacement-side specials for | delimiter.
-# & and \ are replacement-side specials; | is our sed delimiter.
-_esc_sed() { printf '%s\n' "$1" | sed 's/[\\&|]/\\&/g'; }
-
-create_new_agent_file() {
-    local target_file="$1"
-    local temp_file="$2"
-    local project_name
-    project_name=$(_esc_sed "$3")
-    local current_date="$4"
-    
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_error "Template not found at $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    if [[ ! -r "$TEMPLATE_FILE" ]]; then
-        log_error "Template file is not readable: $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    log_info "Creating new agent context file from template..."
-    
-    if ! cp "$TEMPLATE_FILE" "$temp_file"; then
-        log_error "Failed to copy template file"
-        return 1
-    fi
-    
-    # Replace template placeholders
-    local project_structure
-    project_structure=$(get_project_structure "$NEW_PROJECT_TYPE")
-    project_structure=$(_esc_sed "$project_structure")
-    
-    local commands
-    commands=$(get_commands_for_language "$NEW_LANG")
-
-    local language_conventions
-    language_conventions=$(get_language_conventions "$NEW_LANG")
-
-    local escaped_lang=$(_esc_sed "$NEW_LANG")
-    local escaped_framework=$(_esc_sed "$NEW_FRAMEWORK")
-    commands=$(_esc_sed "$commands")
-    language_conventions=$(_esc_sed "$language_conventions")
-    local escaped_branch=$(_esc_sed "$CURRENT_BRANCH")
-    
-    # Build technology stack and recent change strings conditionally
-    local tech_stack
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_lang + $escaped_framework ($escaped_branch)"
-    elif [[ -n "$escaped_lang" ]]; then
-        tech_stack="- $escaped_lang ($escaped_branch)"
-    elif [[ -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_framework ($escaped_branch)"
-    else
-        tech_stack="- ($escaped_branch)"
-    fi
-
-    local recent_change
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang + $escaped_framework"
-    elif [[ -n "$escaped_lang" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang"
-    elif [[ -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_framework"
-    else
-        recent_change="- $escaped_branch: Added"
-    fi
-
-    local substitutions=(
-        "s|\[PROJECT NAME\]|$project_name|"
-        "s|\[DATE\]|$current_date|"
-        "s|\[EXTRACTED FROM ALL PLAN.MD FILES\]|$tech_stack|"
-        "s|\[ACTUAL STRUCTURE FROM PLANS\]|$project_structure|g"
-        "s|\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]|$commands|"
-        "s|\[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE\]|$language_conventions|"
-        "s|\[LAST 3 FEATURES AND WHAT THEY ADDED\]|$recent_change|"
-    )
-    
-    for substitution in "${substitutions[@]}"; do
-        if ! sed -i.bak -e "$substitution" "$temp_file"; then
-            log_error "Failed to perform substitution: $substitution"
-            rm -f "$temp_file" "$temp_file.bak"
-            return 1
-        fi
-    done
-    
-    # Convert literal \n sequences to actual newlines (portable — works on BSD + GNU)
-    awk '{gsub(/\\n/,"\n")}1' "$temp_file" > "$temp_file.tmp"
-    mv "$temp_file.tmp" "$temp_file"
-
-    # Clean up backup files from sed -i.bak
-    rm -f "$temp_file.bak"
-
-    # Prepend Cursor frontmatter for .mdc files so rules are auto-included
-    if [[ "$target_file" == *.mdc ]]; then
-        local frontmatter_file
-        frontmatter_file=$(mktemp) || return 1
-        _CLEANUP_FILES+=("$frontmatter_file")
-        printf '%s\n' "---" "description: Project Development Guidelines" "globs: [\"**/*\"]" "alwaysApply: true" "---" "" > "$frontmatter_file"
-        cat "$temp_file" >> "$frontmatter_file"
-        mv "$frontmatter_file" "$temp_file"
-    fi
-
-    return 0
-}
-
-
-
-
-update_existing_agent_file() {
-    local target_file="$1"
-    local current_date="$2"
-    
-    log_info "Updating existing agent context file..."
-    
-    # Use a single temporary file for atomic update
-    local temp_file
-    temp_file=$(mktemp) || {
-        log_error "Failed to create temporary file"
-        return 1
-    }
-    _CLEANUP_FILES+=("$temp_file")
-    
-    # Process the file in one pass
-    local tech_stack=$(format_technology_stack "$NEW_LANG" "$NEW_FRAMEWORK")
-    local new_tech_entries=()
-    local new_change_entry=""
-    
-    # Prepare new technology entries
-    if [[ -n "$tech_stack" ]] && ! grep -q "$tech_stack" "$target_file"; then
-        new_tech_entries+=("- $tech_stack ($CURRENT_BRANCH)")
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]] && ! grep -q "$NEW_DB" "$target_file"; then
-        new_tech_entries+=("- $NEW_DB ($CURRENT_BRANCH)")
-    fi
-    
-    # Prepare new change entry
-    if [[ -n "$tech_stack" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $tech_stack"
-    elif [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $NEW_DB"
-    fi
-    
-    # Check if sections exist in the file
-    local has_active_technologies=0
-    local has_recent_changes=0
-    
-    if grep -q "^## Active Technologies" "$target_file" 2>/dev/null; then
-        has_active_technologies=1
-    fi
-    
-    if grep -q "^## Recent Changes" "$target_file" 2>/dev/null; then
-        has_recent_changes=1
-    fi
-    
-    # Process file line by line
-    local in_tech_section=false
-    local in_changes_section=false
-    local tech_entries_added=false
-    local changes_entries_added=false
-    local existing_changes_count=0
-    local file_ended=false
-    
-    while IFS= read -r line || [[ -n "$line" ]]; do
-        # Handle Active Technologies section
-        if [[ "$line" == "## Active Technologies" ]]; then
-            echo "$line" >> "$temp_file"
-            in_tech_section=true
-            continue
-        elif [[ $in_tech_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            # Add new tech entries before closing the section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            in_tech_section=false
-            continue
-        elif [[ $in_tech_section == true ]] && [[ -z "$line" ]]; then
-            # Add new tech entries before empty line in tech section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            continue
-        fi
-        
-        # Handle Recent Changes section
-        if [[ "$line" == "## Recent Changes" ]]; then
-            echo "$line" >> "$temp_file"
-            # Add new change entry right after the heading
-            if [[ -n "$new_change_entry" ]]; then
-                echo "$new_change_entry" >> "$temp_file"
-            fi
-            in_changes_section=true
-            changes_entries_added=true
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            echo "$line" >> "$temp_file"
-            in_changes_section=false
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" == "- "* ]]; then
-            # Keep only first 2 existing changes
-            if [[ $existing_changes_count -lt 2 ]]; then
-                echo "$line" >> "$temp_file"
-                ((existing_changes_count++))
-            fi
-            continue
-        fi
-        
-        # Update timestamp
-        if [[ "$line" =~ (\*\*)?Last\ updated(\*\*)?:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
-            echo "$line" | sed "s/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/$current_date/" >> "$temp_file"
-        else
-            echo "$line" >> "$temp_file"
-        fi
-    done < "$target_file"
-    
-    # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
-    if [[ $in_tech_section == true ]] && [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    # If sections don't exist, add them at the end of the file
-    if [[ $has_active_technologies -eq 0 ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        echo "" >> "$temp_file"
-        echo "## Active Technologies" >> "$temp_file"
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    if [[ $has_recent_changes -eq 0 ]] && [[ -n "$new_change_entry" ]]; then
-        echo "" >> "$temp_file"
-        echo "## Recent Changes" >> "$temp_file"
-        echo "$new_change_entry" >> "$temp_file"
-        changes_entries_added=true
-    fi
-    
-    # Ensure Cursor .mdc files have YAML frontmatter for auto-inclusion
-    if [[ "$target_file" == *.mdc ]]; then
-        if ! head -1 "$temp_file" | grep -q '^---'; then
-            local frontmatter_file
-            frontmatter_file=$(mktemp) || { rm -f "$temp_file"; return 1; }
-            _CLEANUP_FILES+=("$frontmatter_file")
-            printf '%s\n' "---" "description: Project Development Guidelines" "globs: [\"**/*\"]" "alwaysApply: true" "---" "" > "$frontmatter_file"
-            cat "$temp_file" >> "$frontmatter_file"
-            mv "$frontmatter_file" "$temp_file"
-        fi
-    fi
-
-    # Move temp file to target atomically
-    if ! mv "$temp_file" "$target_file"; then
-        log_error "Failed to update target file"
-        rm -f "$temp_file"
-        return 1
-    fi
-
-    return 0
-}
-#==============================================================================
-# Main Agent File Update Function
-#==============================================================================
-
-update_agent_file() {
-    local target_file="$1"
-    local agent_name="$2"
-    
-    if [[ -z "$target_file" ]] || [[ -z "$agent_name" ]]; then
-        log_error "update_agent_file requires target_file and agent_name parameters"
-        return 1
-    fi
-    
-    log_info "Updating $agent_name context file: $target_file"
-    
-    local project_name
-    project_name=$(basename "$REPO_ROOT")
-    local current_date
-    current_date=$(date +%Y-%m-%d)
-    
-    # Create directory if it doesn't exist
-    local target_dir
-    target_dir=$(dirname "$target_file")
-    if [[ ! -d "$target_dir" ]]; then
-        if ! mkdir -p "$target_dir"; then
-            log_error "Failed to create directory: $target_dir"
-            return 1
-        fi
-    fi
-    
-    if [[ ! -f "$target_file" ]]; then
-        # Create new file from template
-        local temp_file
-        temp_file=$(mktemp) || {
-            log_error "Failed to create temporary file"
-            return 1
-        }
-        _CLEANUP_FILES+=("$temp_file")
-        
-        if create_new_agent_file "$target_file" "$temp_file" "$project_name" "$current_date"; then
-            if mv "$temp_file" "$target_file"; then
-                log_success "Created new $agent_name context file"
-            else
-                log_error "Failed to move temporary file to $target_file"
-                rm -f "$temp_file"
-                return 1
-            fi
-        else
-            log_error "Failed to create new agent file"
-            rm -f "$temp_file"
-            return 1
-        fi
-    else
-        # Update existing file
-        if [[ ! -r "$target_file" ]]; then
-            log_error "Cannot read existing file: $target_file"
-            return 1
-        fi
-        
-        if [[ ! -w "$target_file" ]]; then
-            log_error "Cannot write to existing file: $target_file"
-            return 1
-        fi
-        
-        if update_existing_agent_file "$target_file" "$current_date"; then
-            log_success "Updated existing $agent_name context file"
-        else
-            log_error "Failed to update existing agent file"
-            return 1
-        fi
-    fi
-    
-    return 0
-}
-
-#==============================================================================
-# Agent Selection and Processing
-#==============================================================================
-
-update_specific_agent() {
-    local agent_type="$1"
-    
-    case "$agent_type" in
-        claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
-            ;;
-        gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI" || return 1
-            ;;
-        copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot" || return 1
-            ;;
-        cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE" || return 1
-            ;;
-        qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code" || return 1
-            ;;
-        opencode)
-            update_agent_file "$AGENTS_FILE" "opencode" || return 1
-            ;;
-        codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI" || return 1
-            ;;
-        windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
-            ;;
-        junie)
-            update_agent_file "$JUNIE_FILE" "Junie" || return 1
-            ;;
-        kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
-            ;;
-        auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI" || return 1
-            ;;
-        roo)
-            update_agent_file "$ROO_FILE" "Roo Code" || return 1
-            ;;
-        codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI" || return 1
-            ;;
-        qodercli)
-            update_agent_file "$QODER_FILE" "Qoder CLI" || return 1
-            ;;
-        amp)
-            update_agent_file "$AMP_FILE" "Amp" || return 1
-            ;;
-        shai)
-            update_agent_file "$SHAI_FILE" "SHAI" || return 1
-            ;;
-        tabnine)
-            update_agent_file "$TABNINE_FILE" "Tabnine CLI" || return 1
-            ;;
-        kiro-cli)
-            update_agent_file "$KIRO_FILE" "Kiro CLI" || return 1
-            ;;
-        agy)
-            update_agent_file "$AGY_FILE" "Antigravity" || return 1
-            ;;
-        bob)
-            update_agent_file "$BOB_FILE" "IBM Bob" || return 1
-            ;;
-        vibe)
-            update_agent_file "$VIBE_FILE" "Mistral Vibe" || return 1
-            ;;
-        kimi)
-            update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
-            ;;
-        trae)
-            update_agent_file "$TRAE_FILE" "Trae" || return 1
-            ;;
-        pi)
-            update_agent_file "$AGENTS_FILE" "Pi Coding Agent" || return 1
-            ;;
-        iflow)
-            update_agent_file "$IFLOW_FILE" "iFlow CLI" || return 1
-            ;;
-        forge)
-            update_agent_file "$AGENTS_FILE" "Forge" || return 1
-            ;;
-        goose)
-            update_agent_file "$AGENTS_FILE" "Goose" || return 1
-            ;;
-        generic)
-            log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
-            ;;
-        *)
-            log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic"
-            exit 1
-            ;;
-    esac
-}
-
-# Helper: skip non-existent files and files already updated (dedup by
-# realpath so that variables pointing to the same file — e.g. AMP_FILE,
-# KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
-# Uses a linear array instead of associative array for bash 3.2 compatibility.
-# Note: defined at top level because bash 3.2 does not support true
-# nested/local functions. _updated_paths, _found_agent, and _all_ok are
-# initialised exclusively inside update_all_existing_agents so that
-# sourcing this script has no side effects on the caller's environment.
-
-_update_if_new() {
-    local file="$1" name="$2"
-    [[ -f "$file" ]] || return 0
-    local real_path
-    real_path=$(realpath "$file" 2>/dev/null || echo "$file")
-    local p
-    if [[ ${#_updated_paths[@]} -gt 0 ]]; then
-        for p in "${_updated_paths[@]}"; do
-            [[ "$p" == "$real_path" ]] && return 0
-        done
-    fi
-    # Record the file as seen before attempting the update so that:
-    # (a) aliases pointing to the same path are not retried on failure
-    # (b) _found_agent reflects file existence, not update success
-    _updated_paths+=("$real_path")
-    _found_agent=true
-    update_agent_file "$file" "$name"
-}
-
-update_all_existing_agents() {
-    _found_agent=false
-    _updated_paths=()
-    local _all_ok=true
-
-    _update_if_new "$CLAUDE_FILE" "Claude Code"           || _all_ok=false
-    _update_if_new "$GEMINI_FILE" "Gemini CLI"             || _all_ok=false
-    _update_if_new "$COPILOT_FILE" "GitHub Copilot"        || _all_ok=false
-    _update_if_new "$CURSOR_FILE" "Cursor IDE"             || _all_ok=false
-    _update_if_new "$QWEN_FILE" "Qwen Code"                || _all_ok=false
-    _update_if_new "$AGENTS_FILE" "Codex/opencode/Amp/Kiro/Bob/Pi/Forge/Goose" || _all_ok=false
-    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
-    _update_if_new "$JUNIE_FILE" "Junie"                || _all_ok=false
-    _update_if_new "$KILOCODE_FILE" "Kilo Code"            || _all_ok=false
-    _update_if_new "$AUGGIE_FILE" "Auggie CLI"             || _all_ok=false
-    _update_if_new "$ROO_FILE" "Roo Code"                  || _all_ok=false
-    _update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"       || _all_ok=false
-    _update_if_new "$SHAI_FILE" "SHAI"                     || _all_ok=false
-    _update_if_new "$TABNINE_FILE" "Tabnine CLI"           || _all_ok=false
-    _update_if_new "$QODER_FILE" "Qoder CLI"               || _all_ok=false
-    _update_if_new "$AGY_FILE" "Antigravity"               || _all_ok=false
-    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
-    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
-    _update_if_new "$TRAE_FILE" "Trae"                     || _all_ok=false
-    _update_if_new "$IFLOW_FILE" "iFlow CLI"               || _all_ok=false
-
-    # If no agent files exist, create a default Claude file
-    if [[ "$_found_agent" == false ]]; then
-        log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
-    fi
-
-    [[ "$_all_ok" == true ]]
-}
-print_summary() {
-    echo
-    log_info "Summary of changes:"
-    
-    if [[ -n "$NEW_LANG" ]]; then
-        echo "  - Added language: $NEW_LANG"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        echo "  - Added framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        echo "  - Added database: $NEW_DB"
-    fi
-    
-    echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic]"
-}
-
-#==============================================================================
-# Main Execution
-#==============================================================================
-
-main() {
-    # Validate environment before proceeding
-    validate_environment
-    
-    log_info "=== Updating agent context files for feature $CURRENT_BRANCH ==="
-    
-    # Parse the plan file to extract project information
-    if ! parse_plan_data "$NEW_PLAN"; then
-        log_error "Failed to parse plan data"
-        exit 1
-    fi
-    
-    # Process based on agent type argument
-    local success=true
-    
-    if [[ -z "$AGENT_TYPE" ]]; then
-        # No specific agent provided - update all existing agent files
-        log_info "No agent specified, updating all existing agent files..."
-        if ! update_all_existing_agents; then
-            success=false
-        fi
-    else
-        # Specific agent provided - update only that agent
-        log_info "Updating specific agent: $AGENT_TYPE"
-        if ! update_specific_agent "$AGENT_TYPE"; then
-            success=false
-        fi
-    fi
-    
-    # Print summary
-    print_summary
-    
-    if [[ "$success" == true ]]; then
-        log_success "Agent context update completed successfully"
-        exit 0
-    else
-        log_error "Agent context update completed with errors"
-        exit 1
-    fi
-}
-
-# Execute main function if script is run directly
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    main "$@"
-fi

scripts/powershell/update-agent-context.ps1

@@ -1,515 +0,0 @@
-#!/usr/bin/env pwsh
-<#!
-.SYNOPSIS
-Update agent context files with information from plan.md (PowerShell version)
-
-.DESCRIPTION
-Mirrors the behavior of scripts/bash/update-agent-context.sh:
- 1. Environment Validation
- 2. Plan Data Extraction
- 3. Agent File Management (create from template or update existing)
- 4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, junie, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, pi, iflow, forge, goose, generic)
-
-.PARAMETER AgentType
-Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
-
-.EXAMPLE
-./update-agent-context.ps1 -AgentType claude
-
-.EXAMPLE
-./update-agent-context.ps1   # Updates all existing agent files
-
-.NOTES
-Relies on common helper functions in common.ps1
-#>
-param(
-    [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','junie','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','vibe','qodercli','kimi','trae','pi','iflow','forge','goose','generic')]
-    [string]$AgentType
-)
-
-$ErrorActionPreference = 'Stop'
-
-# Import common helpers
-$ScriptDir = Split-Path -Parent $MyInvocation.MyCommand.Path
-. (Join-Path $ScriptDir 'common.ps1')
-
-# Acquire environment paths
-$envData = Get-FeaturePathsEnv
-$REPO_ROOT     = $envData.REPO_ROOT
-$CURRENT_BRANCH = $envData.CURRENT_BRANCH
-$HAS_GIT       = $envData.HAS_GIT
-$IMPL_PLAN     = $envData.IMPL_PLAN
-$NEW_PLAN = $IMPL_PLAN
-
-# Agent file paths
-$CLAUDE_FILE   = Join-Path $REPO_ROOT 'CLAUDE.md'
-$GEMINI_FILE   = Join-Path $REPO_ROOT 'GEMINI.md'
-$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/copilot-instructions.md'
-$CURSOR_FILE   = Join-Path $REPO_ROOT '.cursor/rules/specify-rules.mdc'
-$QWEN_FILE     = Join-Path $REPO_ROOT 'QWEN.md'
-$AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'
-$WINDSURF_FILE = Join-Path $REPO_ROOT '.windsurf/rules/specify-rules.md'
-$JUNIE_FILE = Join-Path $REPO_ROOT '.junie/AGENTS.md'
-$KILOCODE_FILE = Join-Path $REPO_ROOT '.kilocode/rules/specify-rules.md'
-$AUGGIE_FILE   = Join-Path $REPO_ROOT '.augment/rules/specify-rules.md'
-$ROO_FILE      = Join-Path $REPO_ROOT '.roo/rules/specify-rules.md'
-$CODEBUDDY_FILE = Join-Path $REPO_ROOT 'CODEBUDDY.md'
-$QODER_FILE    = Join-Path $REPO_ROOT 'QODER.md'
-$AMP_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
-$SHAI_FILE     = Join-Path $REPO_ROOT 'SHAI.md'
-$TABNINE_FILE  = Join-Path $REPO_ROOT 'TABNINE.md'
-$KIRO_FILE     = Join-Path $REPO_ROOT 'AGENTS.md'
-$AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
-$BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
-$VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
-$KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
-$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/project_rules.md'
-$IFLOW_FILE    = Join-Path $REPO_ROOT 'IFLOW.md'
-$FORGE_FILE    = Join-Path $REPO_ROOT 'AGENTS.md'
-$GOOSE_FILE    = Join-Path $REPO_ROOT 'AGENTS.md'
-
-$TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
-
-# Parsed plan data placeholders
-$script:NEW_LANG = ''
-$script:NEW_FRAMEWORK = ''
-$script:NEW_DB = ''
-$script:NEW_PROJECT_TYPE = ''
-
-function Write-Info { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "INFO: $Message" 
-}
-
-function Write-Success { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "$([char]0x2713) $Message" 
-}
-
-function Write-WarningMsg { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Warning $Message 
-}
-
-function Write-Err { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "ERROR: $Message" -ForegroundColor Red 
-}
-
-function Validate-Environment {
-    if (-not $CURRENT_BRANCH) {
-        Write-Err 'Unable to determine current feature'
-        if ($HAS_GIT) { Write-Info "Make sure you're on a feature branch" } else { Write-Info 'Set SPECIFY_FEATURE environment variable or create a feature first' }
-        exit 1
-    }
-    if (-not (Test-Path $NEW_PLAN)) {
-        Write-Err "No plan.md found at $NEW_PLAN"
-        Write-Info 'Ensure you are working on a feature with a corresponding spec directory'
-        if (-not $HAS_GIT) { Write-Info 'Use: $env:SPECIFY_FEATURE=your-feature-name or create a new feature first' }
-        exit 1
-    }
-    if (-not (Test-Path $TEMPLATE_FILE)) {
-        Write-Err "Template file not found at $TEMPLATE_FILE"
-        Write-Info 'Run specify init to scaffold .specify/templates, or add agent-file-template.md there.'
-        exit 1
-    }
-}
-
-function Extract-PlanField {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$FieldPattern,
-        [Parameter(Mandatory=$true)]
-        [string]$PlanFile
-    )
-    if (-not (Test-Path $PlanFile)) { return '' }
-    # Lines like **Language/Version**: Python 3.12
-    $regex = "^\*\*$([Regex]::Escape($FieldPattern))\*\*: (.+)$"
-    Get-Content -LiteralPath $PlanFile -Encoding utf8 | ForEach-Object {
-        if ($_ -match $regex) { 
-            $val = $Matches[1].Trim()
-            if ($val -notin @('NEEDS CLARIFICATION','N/A')) { return $val }
-        }
-    } | Select-Object -First 1
-}
-
-function Parse-PlanData {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$PlanFile
-    )
-    if (-not (Test-Path $PlanFile)) { Write-Err "Plan file not found: $PlanFile"; return $false }
-    Write-Info "Parsing plan data from $PlanFile"
-    $script:NEW_LANG        = Extract-PlanField -FieldPattern 'Language/Version' -PlanFile $PlanFile
-    $script:NEW_FRAMEWORK   = Extract-PlanField -FieldPattern 'Primary Dependencies' -PlanFile $PlanFile
-    $script:NEW_DB          = Extract-PlanField -FieldPattern 'Storage' -PlanFile $PlanFile
-    $script:NEW_PROJECT_TYPE = Extract-PlanField -FieldPattern 'Project Type' -PlanFile $PlanFile
-
-    if ($NEW_LANG) { Write-Info "Found language: $NEW_LANG" } else { Write-WarningMsg 'No language information found in plan' }
-    if ($NEW_FRAMEWORK) { Write-Info "Found framework: $NEW_FRAMEWORK" }
-    if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Info "Found database: $NEW_DB" }
-    if ($NEW_PROJECT_TYPE) { Write-Info "Found project type: $NEW_PROJECT_TYPE" }
-    return $true
-}
-
-function Format-TechnologyStack {
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang,
-        [Parameter(Mandatory=$false)]
-        [string]$Framework
-    )
-    $parts = @()
-    if ($Lang -and $Lang -ne 'NEEDS CLARIFICATION') { $parts += $Lang }
-    if ($Framework -and $Framework -notin @('NEEDS CLARIFICATION','N/A')) { $parts += $Framework }
-    if (-not $parts) { return '' }
-    return ($parts -join ' + ')
-}
-
-function Get-ProjectStructure { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$ProjectType
-    )
-    if ($ProjectType -match 'web') { return "backend/`nfrontend/`ntests/" } else { return "src/`ntests/" } 
-}
-
-function Get-CommandsForLanguage { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang
-    )
-    switch -Regex ($Lang) {
-        'Python' { return "cd src; pytest; ruff check ." }
-        'Rust' { return "cargo test; cargo clippy" }
-        'JavaScript|TypeScript' { return "npm test; npm run lint" }
-        default { return "# Add commands for $Lang" }
-    }
-}
-
-function Get-LanguageConventions { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang
-    )
-    if ($Lang) { "${Lang}: Follow standard conventions" } else { 'General: Follow standard conventions' } 
-}
-
-function New-AgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [string]$ProjectName,
-        [Parameter(Mandatory=$true)]
-        [datetime]$Date
-    )
-    if (-not (Test-Path $TEMPLATE_FILE)) { Write-Err "Template not found at $TEMPLATE_FILE"; return $false }
-    $temp = New-TemporaryFile
-    Copy-Item -LiteralPath $TEMPLATE_FILE -Destination $temp -Force
-
-    $projectStructure = Get-ProjectStructure -ProjectType $NEW_PROJECT_TYPE
-    $commands = Get-CommandsForLanguage -Lang $NEW_LANG
-    $languageConventions = Get-LanguageConventions -Lang $NEW_LANG
-
-    $escaped_lang = $NEW_LANG
-    $escaped_framework = $NEW_FRAMEWORK
-    $escaped_branch = $CURRENT_BRANCH
-
-    $content = Get-Content -LiteralPath $temp -Raw -Encoding utf8
-    $content = $content -replace '\[PROJECT NAME\]',$ProjectName
-    $content = $content -replace '\[DATE\]',$Date.ToString('yyyy-MM-dd')
-    
-    # Build the technology stack string safely
-    $techStackForTemplate = ""
-    if ($escaped_lang -and $escaped_framework) {
-        $techStackForTemplate = "- $escaped_lang + $escaped_framework ($escaped_branch)"
-    } elseif ($escaped_lang) {
-        $techStackForTemplate = "- $escaped_lang ($escaped_branch)"
-    } elseif ($escaped_framework) {
-        $techStackForTemplate = "- $escaped_framework ($escaped_branch)"
-    }
-    
-    $content = $content -replace '\[EXTRACTED FROM ALL PLAN.MD FILES\]',$techStackForTemplate
-    # For project structure we manually embed (keep newlines)
-    $escapedStructure = [Regex]::Escape($projectStructure)
-    $content = $content -replace '\[ACTUAL STRUCTURE FROM PLANS\]',$escapedStructure
-    # Replace escaped newlines placeholder after all replacements
-    $content = $content -replace '\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]',$commands
-    $content = $content -replace '\[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE\]',$languageConventions
-    
-    # Build the recent changes string safely
-    $recentChangesForTemplate = ""
-    if ($escaped_lang -and $escaped_framework) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_lang} + ${escaped_framework}"
-    } elseif ($escaped_lang) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_lang}"
-    } elseif ($escaped_framework) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_framework}"
-    }
-    
-    $content = $content -replace '\[LAST 3 FEATURES AND WHAT THEY ADDED\]',$recentChangesForTemplate
-    # Convert literal \n sequences introduced by Escape to real newlines
-    $content = $content -replace '\\n',[Environment]::NewLine
-
-    # Prepend Cursor frontmatter for .mdc files so rules are auto-included
-    if ($TargetFile -match '\.mdc$') {
-        $frontmatter = @('---','description: Project Development Guidelines','globs: ["**/*"]','alwaysApply: true','---','') -join [Environment]::NewLine
-        $content = $frontmatter + $content
-    }
-
-    $parent = Split-Path -Parent $TargetFile
-    if (-not (Test-Path $parent)) { New-Item -ItemType Directory -Path $parent | Out-Null }
-    Set-Content -LiteralPath $TargetFile -Value $content -NoNewline -Encoding utf8
-    Remove-Item $temp -Force
-    return $true
-}
-
-function Update-ExistingAgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [datetime]$Date
-    )
-    if (-not (Test-Path $TargetFile)) { return (New-AgentFile -TargetFile $TargetFile -ProjectName (Split-Path $REPO_ROOT -Leaf) -Date $Date) }
-
-    $techStack = Format-TechnologyStack -Lang $NEW_LANG -Framework $NEW_FRAMEWORK
-    $newTechEntries = @()
-    if ($techStack) {
-        $escapedTechStack = [Regex]::Escape($techStack)
-        if (-not (Select-String -Pattern $escapedTechStack -Path $TargetFile -Quiet)) { 
-            $newTechEntries += "- $techStack ($CURRENT_BRANCH)" 
-        }
-    }
-    if ($NEW_DB -and $NEW_DB -notin @('N/A','NEEDS CLARIFICATION')) {
-        $escapedDB = [Regex]::Escape($NEW_DB)
-        if (-not (Select-String -Pattern $escapedDB -Path $TargetFile -Quiet)) { 
-            $newTechEntries += "- $NEW_DB ($CURRENT_BRANCH)" 
-        }
-    }
-    $newChangeEntry = ''
-    if ($techStack) { $newChangeEntry = "- ${CURRENT_BRANCH}: Added ${techStack}" }
-    elseif ($NEW_DB -and $NEW_DB -notin @('N/A','NEEDS CLARIFICATION')) { $newChangeEntry = "- ${CURRENT_BRANCH}: Added ${NEW_DB}" }
-
-    $lines = Get-Content -LiteralPath $TargetFile -Encoding utf8
-    $output = New-Object System.Collections.Generic.List[string]
-    $inTech = $false; $inChanges = $false; $techAdded = $false; $changeAdded = $false; $existingChanges = 0
-
-    for ($i=0; $i -lt $lines.Count; $i++) {
-        $line = $lines[$i]
-        if ($line -eq '## Active Technologies') {
-            $output.Add($line)
-            $inTech = $true
-            continue
-        }
-        if ($inTech -and $line -match '^##\s') {
-            if (-not $techAdded -and $newTechEntries.Count -gt 0) { $newTechEntries | ForEach-Object { $output.Add($_) }; $techAdded = $true }
-            $output.Add($line); $inTech = $false; continue
-        }
-        if ($inTech -and [string]::IsNullOrWhiteSpace($line)) {
-            if (-not $techAdded -and $newTechEntries.Count -gt 0) { $newTechEntries | ForEach-Object { $output.Add($_) }; $techAdded = $true }
-            $output.Add($line); continue
-        }
-        if ($line -eq '## Recent Changes') {
-            $output.Add($line)
-            if ($newChangeEntry) { $output.Add($newChangeEntry); $changeAdded = $true }
-            $inChanges = $true
-            continue
-        }
-        if ($inChanges -and $line -match '^##\s') { $output.Add($line); $inChanges = $false; continue }
-        if ($inChanges -and $line -match '^- ') {
-            if ($existingChanges -lt 2) { $output.Add($line); $existingChanges++ }
-            continue
-        }
-        if ($line -match '(\*\*)?Last updated(\*\*)?: .*\d{4}-\d{2}-\d{2}') {
-            $output.Add(($line -replace '\d{4}-\d{2}-\d{2}',$Date.ToString('yyyy-MM-dd')))
-            continue
-        }
-        $output.Add($line)
-    }
-
-    # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
-    if ($inTech -and -not $techAdded -and $newTechEntries.Count -gt 0) {
-        $newTechEntries | ForEach-Object { $output.Add($_) }
-    }
-
-    # Ensure Cursor .mdc files have YAML frontmatter for auto-inclusion
-    if ($TargetFile -match '\.mdc$' -and $output.Count -gt 0 -and $output[0] -ne '---') {
-        $frontmatter = @('---','description: Project Development Guidelines','globs: ["**/*"]','alwaysApply: true','---','')
-        $output.InsertRange(0, $frontmatter)
-    }
-
-    Set-Content -LiteralPath $TargetFile -Value ($output -join [Environment]::NewLine) -Encoding utf8
-    return $true
-}
-
-function Update-AgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [string]$AgentName
-    )
-    if (-not $TargetFile -or -not $AgentName) { Write-Err 'Update-AgentFile requires TargetFile and AgentName'; return $false }
-    Write-Info "Updating $AgentName context file: $TargetFile"
-    $projectName = Split-Path $REPO_ROOT -Leaf
-    $date = Get-Date
-
-    $dir = Split-Path -Parent $TargetFile
-    if (-not (Test-Path $dir)) { New-Item -ItemType Directory -Path $dir | Out-Null }
-
-    if (-not (Test-Path $TargetFile)) {
-        if (New-AgentFile -TargetFile $TargetFile -ProjectName $projectName -Date $date) { Write-Success "Created new $AgentName context file" } else { Write-Err 'Failed to create new agent file'; return $false }
-    } else {
-        try {
-            if (Update-ExistingAgentFile -TargetFile $TargetFile -Date $date) { Write-Success "Updated existing $AgentName context file" } else { Write-Err 'Failed to update agent file'; return $false }
-        } catch {
-            Write-Err "Cannot access or update existing file: $TargetFile. $_"
-            return $false
-        }
-    }
-    return $true
-}
-
-function Update-SpecificAgent {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Type
-    )
-    switch ($Type) {
-        'claude'   { Update-AgentFile -TargetFile $CLAUDE_FILE   -AgentName 'Claude Code' }
-        'gemini'   { Update-AgentFile -TargetFile $GEMINI_FILE   -AgentName 'Gemini CLI' }
-        'copilot'  { Update-AgentFile -TargetFile $COPILOT_FILE  -AgentName 'GitHub Copilot' }
-        'cursor-agent' { Update-AgentFile -TargetFile $CURSOR_FILE   -AgentName 'Cursor IDE' }
-        'qwen'     { Update-AgentFile -TargetFile $QWEN_FILE     -AgentName 'Qwen Code' }
-        'opencode' { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'opencode' }
-        'codex'    { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Codex CLI' }
-        'windsurf' { Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf' }
-        'junie'    { Update-AgentFile -TargetFile $JUNIE_FILE    -AgentName 'Junie' }
-        'kilocode' { Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code' }
-        'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
-        'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
-        'codebuddy' { Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI' }
-        'qodercli' { Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI' }
-        'amp'      { Update-AgentFile -TargetFile $AMP_FILE      -AgentName 'Amp' }
-        'shai'     { Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI' }
-        'tabnine'  { Update-AgentFile -TargetFile $TABNINE_FILE  -AgentName 'Tabnine CLI' }
-        'kiro-cli' { Update-AgentFile -TargetFile $KIRO_FILE     -AgentName 'Kiro CLI' }
-        'agy'      { Update-AgentFile -TargetFile $AGY_FILE      -AgentName 'Antigravity' }
-        'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
-        'vibe'     { Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe' }
-        'kimi'     { Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code' }
-        'trae'     { Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae' }
-        'pi'       { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Pi Coding Agent' }
-        'iflow'    { Update-AgentFile -TargetFile $IFLOW_FILE    -AgentName 'iFlow CLI' }
-        'forge'    { Update-AgentFile -TargetFile $FORGE_FILE    -AgentName 'Forge' }
-        'goose'    { Update-AgentFile -TargetFile $GOOSE_FILE    -AgentName 'Goose' }
-        'generic'  { Write-Info 'Generic agent: no predefined context file. Use the agent-specific update script for your agent.' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic'; return $false }
-    }
-}
-
-function Update-AllExistingAgents {
-    $found = $false
-    $ok = $true
-    $updatedPaths = @()
-    
-    # Helper function to update only if file exists and hasn't been updated yet
-    function Update-IfNew {
-        param(
-            [Parameter(Mandatory=$true)]
-            [string]$FilePath,
-            [Parameter(Mandatory=$true)]
-            [string]$AgentName
-        )
-        
-        if (-not (Test-Path $FilePath)) { return $true }
-        
-        # Get the real path to detect duplicates (e.g., AMP_FILE, KIRO_FILE, BOB_FILE all point to AGENTS.md)
-        $realPath = (Get-Item -LiteralPath $FilePath).FullName
-        
-        # Check if we've already updated this file
-        if ($updatedPaths -contains $realPath) {
-            return $true
-        }
-        
-        # Record the file as seen before attempting the update
-        # Use parent scope (1) to modify Update-AllExistingAgents' local variables
-        Set-Variable -Name updatedPaths -Value ($updatedPaths + $realPath) -Scope 1
-        Set-Variable -Name found -Value $true -Scope 1
-        
-        # Perform the update
-        return (Update-AgentFile -TargetFile $FilePath -AgentName $AgentName)
-    }
-    
-    if (-not (Update-IfNew -FilePath $CLAUDE_FILE   -AgentName 'Claude Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $GEMINI_FILE   -AgentName 'Gemini CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $COPILOT_FILE  -AgentName 'GitHub Copilot')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $CURSOR_FILE   -AgentName 'Cursor IDE')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $QWEN_FILE     -AgentName 'Qwen Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AGENTS_FILE   -AgentName 'Codex/opencode/Amp/Kiro/Bob/Pi/Forge/Goose')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $WINDSURF_FILE -AgentName 'Windsurf')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $JUNIE_FILE    -AgentName 'Junie')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $KILOCODE_FILE -AgentName 'Kilo Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AUGGIE_FILE   -AgentName 'Auggie CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $ROO_FILE      -AgentName 'Roo Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $QODER_FILE    -AgentName 'Qoder CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $SHAI_FILE     -AgentName 'SHAI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $TABNINE_FILE  -AgentName 'Tabnine CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AGY_FILE      -AgentName 'Antigravity')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $VIBE_FILE     -AgentName 'Mistral Vibe')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $KIMI_FILE     -AgentName 'Kimi Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $TRAE_FILE     -AgentName 'Trae')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $IFLOW_FILE    -AgentName 'iFlow CLI')) { $ok = $false }
-    
-    if (-not $found) {
-        Write-Info 'No existing agent files found, creating default Claude file...'
-        if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
-    }
-    return $ok
-}
-
-function Print-Summary {
-    Write-Host ''
-    Write-Info 'Summary of changes:'
-    if ($NEW_LANG) { Write-Host "  - Added language: $NEW_LANG" }
-    if ($NEW_FRAMEWORK) { Write-Host "  - Added framework: $NEW_FRAMEWORK" }
-    if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Host "  - Added database: $NEW_DB" }
-    Write-Host ''
-    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic]'
-}
-
-function Main {
-    Validate-Environment
-    Write-Info "=== Updating agent context files for feature $CURRENT_BRANCH ==="
-    if (-not (Parse-PlanData -PlanFile $NEW_PLAN)) { Write-Err 'Failed to parse plan data'; exit 1 }
-    $success = $true
-    if ($AgentType) {
-        Write-Info "Updating specific agent: $AgentType"
-        if (-not (Update-SpecificAgent -Type $AgentType)) { $success = $false }
-    }
-    else {
-        Write-Info 'No agent specified, updating all existing agent files...'
-        if (-not (Update-AllExistingAgents)) { $success = $false }
-    }
-    Print-Summary
-    if ($success) { Write-Success 'Agent context update completed successfully'; exit 0 } else { Write-Err 'Agent context update completed with errors'; exit 1 }
-}
-
-Main

src/specify_cli/__init__.py

@@ -1261,15 +1261,11 @@ def init(
             manifest.save()
 
             # Write .specify/integration.json
-            script_ext = "sh" if selected_script == "sh" else "ps1"
             integration_json = project_path / ".specify" / "integration.json"
             integration_json.parent.mkdir(parents=True, exist_ok=True)
             integration_json.write_text(json.dumps({
                 "integration": resolved_integration.key,
                 "version": get_speckit_version(),
-                "scripts": {
-                    "update-context": f".specify/integrations/{resolved_integration.key}/scripts/update-context.{script_ext}",
-                },
             }, indent=2) + "\n", encoding="utf-8")
 
             tracker.complete("integration", resolved_integration.config.get("name", resolved_integration.key))
@@ -1373,6 +1369,7 @@ def init(
                 "ai": selected_ai,
                 "integration": resolved_integration.key,
                 "branch_numbering": branch_numbering or "sequential",
+                "context_file": resolved_integration.context_file,
                 "here": here,
                 "preset": preset,
                 "script": selected_script,
@@ -1737,18 +1734,13 @@ def _read_integration_json(project_root: Path) -> dict[str, Any]:
 def _write_integration_json(
     project_root: Path,
     integration_key: str,
-    script_type: str,
 ) -> None:
     """Write ``.specify/integration.json`` for *integration_key*."""
-    script_ext = "sh" if script_type == "sh" else "ps1"
     dest = project_root / INTEGRATION_JSON
     dest.parent.mkdir(parents=True, exist_ok=True)
     dest.write_text(json.dumps({
         "integration": integration_key,
         "version": get_speckit_version(),
-        "scripts": {
-            "update-context": f".specify/integrations/{integration_key}/scripts/update-context.{script_ext}",
-        },
     }, indent=2) + "\n", encoding="utf-8")
 
 
@@ -1936,7 +1928,7 @@ def integration_install(
             raw_options=integration_options,
         )
         manifest.save()
-        _write_integration_json(project_root, integration.key, selected_script)
+        _write_integration_json(project_root, integration.key)
         _update_init_options_for_integration(project_root, integration, script_type=selected_script)
 
     except Exception as e:
@@ -2013,6 +2005,7 @@ def _update_init_options_for_integration(
     opts = load_init_options(project_root)
     opts["integration"] = integration.key
     opts["ai"] = integration.key
+    opts["context_file"] = integration.context_file
     if script_type:
         opts["script"] = script_type
     if isinstance(integration, SkillsIntegration):
@@ -2064,6 +2057,7 @@ def integration_uninstall(
             opts.pop("integration", None)
             opts.pop("ai", None)
             opts.pop("ai_skills", None)
+            opts.pop("context_file", None)
             save_init_options(project_root, opts)
         raise typer.Exit(0)
 
@@ -2082,6 +2076,10 @@ def integration_uninstall(
 
     removed, skipped = manifest.uninstall(project_root, force=force)
 
+    # Remove managed context section from the agent context file
+    if integration:
+        integration.remove_context_section(project_root)
+
     _remove_integration_json(project_root)
 
     # Update init-options.json to clear the integration
@@ -2090,6 +2088,7 @@ def integration_uninstall(
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
+        opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
     name = (integration.config or {}).get("name", key) if integration else key
@@ -2156,6 +2155,7 @@ def integration_switch(
                 )
                 raise typer.Exit(1)
             removed, skipped = old_manifest.uninstall(project_root, force=force)
+            current_integration.remove_context_section(project_root)
             if removed:
                 console.print(f"  Removed {len(removed)} file(s)")
             if skipped:
@@ -2186,6 +2186,7 @@ def integration_switch(
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
+        opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
     # Ensure shared infrastructure is present (safe to run unconditionally;
@@ -2212,7 +2213,7 @@ def integration_switch(
             raw_options=integration_options,
         )
         manifest.save()
-        _write_integration_json(project_root, target_integration.key, selected_script)
+        _write_integration_json(project_root, target_integration.key)
         _update_init_options_for_integration(project_root, target_integration, script_type=selected_script)
 
     except Exception as e:
@@ -2320,7 +2321,7 @@ def integration_upgrade(
             raw_options=integration_options,
         )
         new_manifest.save()
-        _write_integration_json(project_root, key, selected_script)
+        _write_integration_json(project_root, key)
         _update_init_options_for_integration(project_root, integration, script_type=selected_script)
     except Exception as exc:
         # Don't teardown — setup overwrites in-place, so teardown would

src/specify_cli/agents.py

@@ -110,9 +110,9 @@ class CommandRegistrar:
         """Normalize script paths in frontmatter to generated project locations.
 
         Rewrites known repo-relative and top-level script paths under the
-        `scripts` and `agent_scripts` keys (for example `../../scripts/`,
-        `../../templates/`, `../../memory/`, `scripts/`, `templates/`, and
-        `memory/`) to the `.specify/...` paths used in generated projects.
+        ``scripts`` key (for example ``../../scripts/``,
+        ``../../templates/``, ``../../memory/``, ``scripts/``, ``templates/``, and
+        ``memory/``) to the ``.specify/...`` paths used in generated projects.
 
         Args:
             frontmatter: Frontmatter dictionary
@@ -122,11 +122,8 @@ class CommandRegistrar:
         """
         frontmatter = deepcopy(frontmatter)
 
-        for script_key in ("scripts", "agent_scripts"):
-            scripts = frontmatter.get(script_key)
-            if not isinstance(scripts, dict):
-                continue
-
+        scripts = frontmatter.get("scripts")
+        if isinstance(scripts, dict):
             for key, script_path in scripts.items():
                 if isinstance(script_path, str):
                     scripts[key] = self.rewrite_project_relative_paths(script_path)
@@ -333,11 +330,8 @@ class CommandRegistrar:
             frontmatter = {}
 
         scripts = frontmatter.get("scripts", {}) or {}
-        agent_scripts = frontmatter.get("agent_scripts", {}) or {}
         if not isinstance(scripts, dict):
             scripts = {}
-        if not isinstance(agent_scripts, dict):
-            agent_scripts = {}
 
         init_opts = load_init_options(project_root)
         if not isinstance(init_opts, dict):
@@ -351,17 +345,14 @@ class CommandRegistrar:
             )
             secondary_variant = "sh" if default_variant == "ps" else "ps"
 
-            if default_variant in scripts or default_variant in agent_scripts:
+            if default_variant in scripts:
                 fallback_order.append(default_variant)
-            if secondary_variant in scripts or secondary_variant in agent_scripts:
+            if secondary_variant in scripts:
                 fallback_order.append(secondary_variant)
 
             for key in scripts:
                 if key not in fallback_order:
                     fallback_order.append(key)
-            for key in agent_scripts:
-                if key not in fallback_order:
-                    fallback_order.append(key)
 
             script_variant = fallback_order[0] if fallback_order else None
 
@@ -370,14 +361,12 @@ class CommandRegistrar:
             script_command = script_command.replace("{ARGS}", "$ARGUMENTS")
             body = body.replace("{SCRIPT}", script_command)
 
-        agent_script_command = (
-            agent_scripts.get(script_variant) if script_variant else None
-        )
-        if agent_script_command:
-            agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
-            body = body.replace("{AGENT_SCRIPT}", agent_script_command)
-
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
+
+        # Resolve __CONTEXT_FILE__ from init-options
+        context_file = init_opts.get("context_file") or ""
+        body = body.replace("__CONTEXT_FILE__", context_file)
+
         return CommandRegistrar.rewrite_project_relative_paths(body)
 
     def _convert_argument_placeholder(

src/specify_cli/integrations/agy/scripts/update-context.ps1

@@ -1,17 +0,0 @@
-# update-context.ps1 — Antigravity (agy) integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType agy

src/specify_cli/integrations/agy/scripts/update-context.sh

@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Antigravity (agy) integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" agy

src/specify_cli/integrations/amp/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Amp integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType amp

src/specify_cli/integrations/amp/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Amp integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" amp

src/specify_cli/integrations/auggie/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Auggie CLI integration: create/update .augment/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType auggie

src/specify_cli/integrations/auggie/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Auggie CLI integration: create/update .augment/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" auggie

src/specify_cli/integrations/base.py

@@ -84,6 +84,11 @@ class IntegrationBase(ABC):
     context_file: str | None = None
     """Relative path to the agent context file (e.g. ``CLAUDE.md``)."""
 
+    # -- Markers for managed context section ------------------------------
+
+    CONTEXT_MARKER_START = "<!-- SPECKIT START -->"
+    CONTEXT_MARKER_END = "<!-- SPECKIT END -->"
+
     # -- Public API -------------------------------------------------------
 
     @classmethod
@@ -380,22 +385,235 @@ class IntegrationBase(ABC):
 
         return created
 
+    # -- Agent context file management ------------------------------------
+
+    @staticmethod
+    def _ensure_mdc_frontmatter(content: str) -> str:
+        """Ensure ``.mdc`` content has YAML frontmatter with ``alwaysApply: true``.
+
+        If frontmatter is missing, prepend it.  If frontmatter exists but
+        ``alwaysApply`` is absent or not ``true``, inject/fix it.
+
+        Uses string/regex manipulation to preserve comments and formatting
+        in existing frontmatter.
+        """
+        import re as _re
+
+        leading_ws = len(content) - len(content.lstrip())
+        leading = content[:leading_ws]
+        stripped = content[leading_ws:]
+
+        if not stripped.startswith("---"):
+            return "---\nalwaysApply: true\n---\n\n" + content
+
+        # Match frontmatter block: ---\n...\n---
+        match = _re.match(
+            r"^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)",
+            stripped,
+            _re.DOTALL,
+        )
+        if not match:
+            return "---\nalwaysApply: true\n---\n\n" + content
+
+        opening, fm_text, closing, sep, rest = match.groups()
+        newline = "\r\n" if "\r\n" in opening else "\n"
+
+        # Already correct?
+        if _re.search(
+            r"(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$", fm_text
+        ):
+            return content
+
+        # alwaysApply exists but wrong value — fix in place while preserving
+        # indentation and any trailing inline comment.
+        if _re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:", fm_text):
+            fm_text = _re.sub(
+                r"(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$",
+                r"\1alwaysApply: true\2",
+                fm_text,
+                count=1,
+            )
+        elif fm_text.strip():
+            fm_text = fm_text + newline + "alwaysApply: true"
+        else:
+            fm_text = "alwaysApply: true"
+
+        return f"{leading}{opening}{fm_text}{closing}{sep}{rest}"
+
+    @staticmethod
+    def _build_context_section(plan_path: str = "") -> str:
+        """Build the content for the managed section between markers.
+
+        *plan_path* is the project-relative path to the current plan
+        (e.g. ``"specs/<feature>/plan.md"``).  When empty, the section
+        contains only the generic directive without a concrete path.
+        """
+        lines = [
+            "For additional context about technologies to be used, project structure,",
+            "shell commands, and other important information, read the current plan",
+        ]
+        if plan_path:
+            lines.append(f"at {plan_path}")
+        return "\n".join(lines)
+
+    def upsert_context_section(
+        self,
+        project_root: Path,
+        plan_path: str = "",
+    ) -> Path | None:
+        """Create or update the managed section in the agent context file.
+
+        If the context file does not exist it is created with just the
+        managed section.  If it exists, the content between
+        ``<!-- SPECKIT START -->`` and ``<!-- SPECKIT END -->`` markers
+        is replaced (or appended when no markers are found).
+
+        Returns the path to the context file, or ``None`` when
+        ``context_file`` is not set.
+        """
+        if not self.context_file:
+            return None
+
+        ctx_path = project_root / self.context_file
+        section = (
+            f"{self.CONTEXT_MARKER_START}\n"
+            f"{self._build_context_section(plan_path)}\n"
+            f"{self.CONTEXT_MARKER_END}\n"
+        )
+
+        if ctx_path.exists():
+            content = ctx_path.read_text(encoding="utf-8")
+            start_idx = content.find(self.CONTEXT_MARKER_START)
+            end_idx = content.find(
+                self.CONTEXT_MARKER_END,
+                start_idx if start_idx != -1 else 0,
+            )
+
+            if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
+                # Replace existing section (include the end marker + newline)
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                # Consume trailing line ending (CRLF or LF)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
+                if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                    end_of_marker += 1
+                new_content = content[:start_idx] + section + content[end_of_marker:]
+            elif start_idx != -1:
+                # Corrupted: start marker without end — replace from start through EOF
+                new_content = content[:start_idx] + section
+            elif end_idx != -1:
+                # Corrupted: end marker without start — replace BOF through end marker
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
+                if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                    end_of_marker += 1
+                new_content = section + content[end_of_marker:]
+            else:
+                # No markers found — append
+                if content:
+                    if not content.endswith("\n"):
+                        content += "\n"
+                    new_content = content + "\n" + section
+                else:
+                    new_content = section
+
+            # Ensure .mdc files have required YAML frontmatter
+            if ctx_path.suffix == ".mdc":
+                new_content = self._ensure_mdc_frontmatter(new_content)
+        else:
+            ctx_path.parent.mkdir(parents=True, exist_ok=True)
+            # Cursor .mdc files require YAML frontmatter to be loaded
+            if ctx_path.suffix == ".mdc":
+                new_content = self._ensure_mdc_frontmatter(section)
+            else:
+                new_content = section
+
+        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
+        ctx_path.write_bytes(normalized.encode("utf-8"))
+        return ctx_path
+
+    def remove_context_section(self, project_root: Path) -> bool:
+        """Remove the managed section from the agent context file.
+
+        Returns ``True`` if the section was found and removed.  If the
+        file becomes empty (or whitespace-only) after removal it is
+        deleted.
+        """
+        if not self.context_file:
+            return False
+
+        ctx_path = project_root / self.context_file
+        if not ctx_path.exists():
+            return False
+
+        content = ctx_path.read_text(encoding="utf-8")
+        start_idx = content.find(self.CONTEXT_MARKER_START)
+        end_idx = content.find(
+            self.CONTEXT_MARKER_END,
+            start_idx if start_idx != -1 else 0,
+        )
+
+        # Only remove a complete, well-ordered managed section. If either
+        # marker is missing, leave the file unchanged to avoid deleting
+        # unrelated user-authored content.
+        if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
+            return False
+
+        removal_start = start_idx
+        removal_end = end_idx + len(self.CONTEXT_MARKER_END)
+
+        # Consume trailing line ending (CRLF or LF)
+        if removal_end < len(content) and content[removal_end] == "\r":
+            removal_end += 1
+        if removal_end < len(content) and content[removal_end] == "\n":
+            removal_end += 1
+
+        # Also strip a blank line before the section if present
+        if removal_start > 0 and content[removal_start - 1] == "\n":
+            if removal_start > 1 and content[removal_start - 2] == "\n":
+                removal_start -= 1
+
+        new_content = content[:removal_start] + content[removal_end:]
+
+        # Normalize line endings before comparisons
+        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
+
+        # For .mdc files, treat Speckit-generated frontmatter-only content as empty
+        if ctx_path.suffix == ".mdc":
+            import re
+            # Delete the file if only YAML frontmatter remains (no body content)
+            frontmatter_only = re.match(
+                r"^---\n.*?\n---\s*$", normalized, re.DOTALL
+            )
+            if not normalized.strip() or frontmatter_only:
+                ctx_path.unlink()
+                return True
+
+        if not normalized.strip():
+            ctx_path.unlink()
+        else:
+            ctx_path.write_bytes(normalized.encode("utf-8"))
+
+        return True
+
     @staticmethod
     def process_template(
         content: str,
         agent_name: str,
         script_type: str,
         arg_placeholder: str = "$ARGUMENTS",
+        context_file: str = "",
     ) -> str:
         """Process a raw command template into agent-ready content.
 
         Performs the same transformations as the release script:
         1. Extract ``scripts.<script_type>`` value from YAML frontmatter
         2. Replace ``{SCRIPT}`` with the extracted script command
-        3. Extract ``agent_scripts.<script_type>`` and replace ``{AGENT_SCRIPT}``
-        4. Strip ``scripts:`` and ``agent_scripts:`` sections from frontmatter
-        5. Replace ``{ARGS}`` and ``$ARGUMENTS`` with *arg_placeholder*
-        6. Replace ``__AGENT__`` with *agent_name*
+        3. Strip ``scripts:`` section from frontmatter
+        4. Replace ``{ARGS}`` and ``$ARGUMENTS`` with *arg_placeholder*
+        5. Replace ``__AGENT__`` with *agent_name*
+        6. Replace ``__CONTEXT_FILE__`` with *context_file*
         7. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
         """
         # 1. Extract script command from frontmatter
@@ -421,25 +639,7 @@ class IntegrationBase(ABC):
         if script_command:
             content = content.replace("{SCRIPT}", script_command)
 
-        # 3. Extract agent_script command
-        agent_script_command = ""
-        in_agent_scripts = False
-        for line in content.splitlines():
-            if line.strip() == "agent_scripts:":
-                in_agent_scripts = True
-                continue
-            if in_agent_scripts and line and not line[0].isspace():
-                in_agent_scripts = False
-            if in_agent_scripts:
-                m = script_pattern.match(line)
-                if m:
-                    agent_script_command = m.group(1).strip()
-                    break
-
-        if agent_script_command:
-            content = content.replace("{AGENT_SCRIPT}", agent_script_command)
-
-        # 4. Strip scripts: and agent_scripts: sections from frontmatter
+        # 3. Strip scripts: section from frontmatter
         lines = content.splitlines(keepends=True)
         output_lines: list[str] = []
         in_frontmatter = False
@@ -457,23 +657,26 @@ class IntegrationBase(ABC):
                 output_lines.append(line)
                 continue
             if in_frontmatter:
-                if stripped in ("scripts:", "agent_scripts:"):
+                if stripped == "scripts:":
                     skip_section = True
                     continue
                 if skip_section:
                     if line[0:1].isspace():
-                        continue  # skip indented content under scripts/agent_scripts
+                        continue  # skip indented content under scripts
                     skip_section = False
             output_lines.append(line)
         content = "".join(output_lines)
 
-        # 5. Replace {ARGS} and $ARGUMENTS
+        # 4. Replace {ARGS} and $ARGUMENTS
         content = content.replace("{ARGS}", arg_placeholder)
         content = content.replace("$ARGUMENTS", arg_placeholder)
 
-        # 6. Replace __AGENT__
+        # 5. Replace __AGENT__
         content = content.replace("__AGENT__", agent_name)
 
+        # 6. Replace __CONTEXT_FILE__
+        content = content.replace("__CONTEXT_FILE__", context_file)
+
         # 7. Rewrite paths — delegate to the shared implementation in
         #    CommandRegistrar so extension-local paths are preserved and
         #    boundary rules stay consistent across the codebase.
@@ -526,6 +729,9 @@ class IntegrationBase(ABC):
             self.record_file_in_manifest(dst_file, project_root, manifest)
             created.append(dst_file)
 
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
     def teardown(
@@ -539,9 +745,11 @@ class IntegrationBase(ABC):
 
         Delegates to ``manifest.uninstall()`` which only removes files
         whose hash still matches the recorded value (unless *force*).
+        Also removes the managed context section from the agent file.
 
         Returns ``(removed, skipped)`` file lists.
         """
+        self.remove_context_section(project_root)
         return manifest.uninstall(project_root, force=force)
 
     # -- Convenience helpers for subclasses -------------------------------
@@ -579,8 +787,8 @@ class MarkdownIntegration(IntegrationBase):
     (and optionally ``context_file``).  Everything else is inherited.
 
     ``setup()`` processes command templates (replacing ``{SCRIPT}``,
-    ``{ARGS}``, ``__AGENT__``, rewriting paths) and installs
-    integration-specific scripts (``update-context.sh`` / ``.ps1``).
+    ``{ARGS}``, ``__AGENT__``, rewriting paths) and upserts the
+    managed context section into the agent context file.
     """
 
     def build_exec_args(
@@ -638,7 +846,8 @@ class MarkdownIntegration(IntegrationBase):
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -646,7 +855,9 @@ class MarkdownIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -841,7 +1052,8 @@ class TomlIntegration(IntegrationBase):
             raw = src_file.read_text(encoding="utf-8")
             description = self._extract_description(raw)
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             toml_content = self._render_toml(description, body)
@@ -851,7 +1063,9 @@ class TomlIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -1021,7 +1235,8 @@ class YamlIntegration(IntegrationBase):
                 title = self._human_title(src_file.stem)
 
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             yaml_content = self._render_yaml(
@@ -1033,7 +1248,9 @@ class YamlIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -1176,7 +1393,8 @@ class SkillsIntegration(IntegrationBase):
 
             # Process body through the standard template pipeline
             processed_body = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             # Strip the processed frontmatter — we rebuild it for skills.
             # Preserve leading whitespace in the body to match release ZIP
@@ -1220,5 +1438,7 @@ class SkillsIntegration(IntegrationBase):
             )
             created.append(dst)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created

src/specify_cli/integrations/bob/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — IBM Bob integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType bob

src/specify_cli/integrations/bob/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — IBM Bob integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" bob

src/specify_cli/integrations/claude/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Claude Code integration: create/update CLAUDE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType claude

src/specify_cli/integrations/claude/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Claude Code integration: create/update CLAUDE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" claude

src/specify_cli/integrations/codebuddy/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — CodeBuddy integration: create/update CODEBUDDY.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType codebuddy

src/specify_cli/integrations/codebuddy/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — CodeBuddy integration: create/update CODEBUDDY.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" codebuddy

src/specify_cli/integrations/codex/scripts/update-context.ps1

@@ -1,17 +0,0 @@
-# update-context.ps1 — Codex CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType codex

src/specify_cli/integrations/codex/scripts/update-context.sh

@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Codex CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" codex

src/specify_cli/integrations/copilot/__init__.py

@@ -183,7 +183,10 @@ class CopilotIntegration(IntegrationBase):
         # 1. Process and write command files as .agent.md
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
                 processed, dest / dst_name, project_root, manifest
@@ -217,8 +220,8 @@ class CopilotIntegration(IntegrationBase):
                 self.record_file_in_manifest(dst_settings, project_root, manifest)
                 created.append(dst_settings)
 
-        # 4. Install integration-specific update-context scripts
-        created.extend(self.install_scripts(project_root, manifest))
+        # 4. Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
 
         return created
 

src/specify_cli/integrations/copilot/scripts/update-context.ps1

@@ -1,32 +0,0 @@
-# update-context.ps1 — Copilot integration: create/update .github/copilot-instructions.md
-#
-# This is the copilot-specific implementation that produces the GitHub
-# Copilot instructions file. The shared dispatcher reads
-# .specify/integration.json and calls this script.
-#
-# NOTE: This script is not yet active. It will be activated in Stage 7
-# when the shared update-agent-context.ps1 replaces its switch statement
-# with integration.json-based dispatch. The shared script must also be
-# refactored to support SPECKIT_SOURCE_ONLY (guard the Main call) before
-# dot-sourcing will work.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-# Invoke shared update-agent-context script as a separate process.
-# Dot-sourcing is unsafe until that script guards its Main call.
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType copilot

src/specify_cli/integrations/copilot/scripts/update-context.sh

@@ -1,37 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Copilot integration: create/update .github/copilot-instructions.md
-#
-# This is the copilot-specific implementation that produces the GitHub
-# Copilot instructions file. The shared dispatcher reads
-# .specify/integration.json and calls this script.
-#
-# NOTE: This script is not yet active. It will be activated in Stage 7
-# when the shared update-agent-context.sh replaces its case statement
-# with integration.json-based dispatch. The shared script must also be
-# refactored to support SPECKIT_SOURCE_ONLY (guard the main logic)
-# before sourcing will work.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-# Invoke shared update-agent-context script as a separate process.
-# Sourcing is unsafe until that script guards its main logic.
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" copilot

src/specify_cli/integrations/cursor_agent/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Cursor integration: create/update .cursor/rules/specify-rules.mdc
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType cursor-agent

src/specify_cli/integrations/cursor_agent/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Cursor integration: create/update .cursor/rules/specify-rules.mdc
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" cursor-agent

src/specify_cli/integrations/forge/__init__.py

@@ -130,7 +130,10 @@ class ForgeIntegration(MarkdownIntegration):
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             # Process template with standard MarkdownIntegration logic
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
 
             # FORGE-SPECIFIC: Ensure any remaining $ARGUMENTS placeholders are
             # converted to {{parameters}}
@@ -145,8 +148,8 @@ class ForgeIntegration(MarkdownIntegration):
             )
             created.append(dst_file)
 
-        # Install integration-specific update-context scripts
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
 
         return created
 

src/specify_cli/integrations/forge/scripts/update-context.ps1

@@ -1,33 +0,0 @@
-# update-context.ps1 — Forge integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-$sharedScript = "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if (-not (Test-Path $sharedScript)) {
-    Write-Error "Error: shared agent context updater not found: $sharedScript"
-    Write-Error "Forge integration requires support in scripts/powershell/update-agent-context.ps1."
-    exit 1
-}
-
-& $sharedScript -AgentType forge
-exit $LASTEXITCODE

src/specify_cli/integrations/forge/scripts/update-context.sh

@@ -1,38 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Forge integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-shared_script="$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if [ ! -x "$shared_script" ]; then
-  echo "Error: shared agent context updater not found or not executable:" >&2
-  echo "  $shared_script" >&2
-  echo "Forge integration requires support in scripts/bash/update-agent-context.sh." >&2
-  exit 1
-fi
-
-exec "$shared_script" forge

src/specify_cli/integrations/gemini/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Gemini CLI integration: create/update GEMINI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType gemini

src/specify_cli/integrations/gemini/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Gemini CLI integration: create/update GEMINI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" gemini

src/specify_cli/integrations/generic/__init__.py

@@ -31,7 +31,7 @@ class GenericIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = None
+    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -122,12 +122,17 @@ class GenericIntegration(MarkdownIntegration):
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
                 processed, dest / dst_name, project_root, manifest
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created

src/specify_cli/integrations/generic/scripts/update-context.ps1

@@ -1,17 +0,0 @@
-# update-context.ps1 — Generic integration: create/update context file
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType generic

src/specify_cli/integrations/generic/scripts/update-context.sh

@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Generic integration: create/update context file
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" generic

src/specify_cli/integrations/goose/scripts/update-context.ps1

@@ -1,33 +0,0 @@
-# update-context.ps1 — Goose integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-$sharedScript = "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if (-not (Test-Path $sharedScript)) {
-    Write-Error "Error: shared agent context updater not found: $sharedScript"
-    Write-Error "Goose integration requires support in scripts/powershell/update-agent-context.ps1."
-    exit 1
-}
-
-& $sharedScript -AgentType goose
-exit $LASTEXITCODE

src/specify_cli/integrations/goose/scripts/update-context.sh

@@ -1,38 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Goose integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-shared_script="$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if [ ! -x "$shared_script" ]; then
-  echo "Error: shared agent context updater not found or not executable:" >&2
-  echo "  $shared_script" >&2
-  echo "Goose integration requires support in scripts/bash/update-agent-context.sh." >&2
-  exit 1
-fi
-
-exec "$shared_script" goose

src/specify_cli/integrations/iflow/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — iFlow CLI integration: create/update IFLOW.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType iflow

src/specify_cli/integrations/iflow/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — iFlow CLI integration: create/update IFLOW.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" iflow

src/specify_cli/integrations/junie/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Junie integration: create/update .junie/AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType junie

src/specify_cli/integrations/junie/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Junie integration: create/update .junie/AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" junie

src/specify_cli/integrations/kilocode/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Kilo Code integration: create/update .kilocode/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kilocode

src/specify_cli/integrations/kilocode/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kilo Code integration: create/update .kilocode/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kilocode

src/specify_cli/integrations/kimi/scripts/update-context.ps1

@@ -1,17 +0,0 @@
-# update-context.ps1 — Kimi Code integration: create/update KIMI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kimi

src/specify_cli/integrations/kimi/scripts/update-context.sh

@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kimi Code integration: create/update KIMI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kimi

src/specify_cli/integrations/kiro_cli/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Kiro CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kiro-cli

src/specify_cli/integrations/kiro_cli/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kiro CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kiro-cli

src/specify_cli/integrations/opencode/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — opencode integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType opencode

src/specify_cli/integrations/opencode/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — opencode integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" opencode

src/specify_cli/integrations/pi/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Pi Coding Agent integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType pi

src/specify_cli/integrations/pi/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Pi Coding Agent integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" pi

src/specify_cli/integrations/qodercli/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Qoder CLI integration: create/update QODER.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType qodercli

src/specify_cli/integrations/qodercli/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Qoder CLI integration: create/update QODER.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" qodercli

src/specify_cli/integrations/qwen/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Qwen Code integration: create/update QWEN.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType qwen

src/specify_cli/integrations/qwen/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Qwen Code integration: create/update QWEN.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" qwen

src/specify_cli/integrations/roo/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Roo Code integration: create/update .roo/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType roo

src/specify_cli/integrations/roo/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Roo Code integration: create/update .roo/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" roo

src/specify_cli/integrations/shai/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — SHAI integration: create/update SHAI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType shai

src/specify_cli/integrations/shai/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — SHAI integration: create/update SHAI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" shai

src/specify_cli/integrations/tabnine/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Tabnine CLI integration: create/update TABNINE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType tabnine

src/specify_cli/integrations/tabnine/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Tabnine CLI integration: create/update TABNINE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" tabnine

src/specify_cli/integrations/trae/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Trae integration: create/update .trae/rules/project_rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType trae

src/specify_cli/integrations/trae/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Trae integration: create/update .trae/rules/project_rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" trae

src/specify_cli/integrations/vibe/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Mistral Vibe integration: create/update .vibe/agents/specify-agents.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType vibe

src/specify_cli/integrations/vibe/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Mistral Vibe integration: create/update .vibe/agents/specify-agents.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" vibe

src/specify_cli/integrations/windsurf/scripts/update-context.ps1

@@ -1,23 +0,0 @@
-# update-context.ps1 — Windsurf integration: create/update .windsurf/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType windsurf

src/specify_cli/integrations/windsurf/scripts/update-context.sh

@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Windsurf integration: create/update .windsurf/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" windsurf

templates/agent-file-template.md

@@ -1,28 +0,0 @@
-# [PROJECT NAME] Development Guidelines
-
-Auto-generated from all feature plans. Last updated: [DATE]
-
-## Active Technologies
-
-[EXTRACTED FROM ALL PLAN.MD FILES]
-
-## Project Structure
-
-```text
-[ACTUAL STRUCTURE FROM PLANS]
-```
-
-## Commands
-
-[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES]
-
-## Code Style
-
-[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE]
-
-## Recent Changes
-
-[LAST 3 FEATURES AND WHAT THEY ADDED]
-
-<!-- MANUAL ADDITIONS START -->
-<!-- MANUAL ADDITIONS END -->

templates/commands/plan.md

@@ -11,9 +11,6 @@ handoffs:
 scripts:
   sh: scripts/bash/setup-plan.sh --json
   ps: scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: scripts/bash/update-agent-context.sh __AGENT__
-  ps: scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 ## User Input
@@ -145,15 +142,11 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Skip if project is purely internal (build scripts, one-off tools, etc.)
 
 3. **Agent context update**:
-   - Run `{AGENT_SCRIPT}`
-   - These scripts detect which AI agent is in use
-   - Update the appropriate agent-specific context file
-   - Add only new technology from current plan
-   - Preserve manual additions between markers
+   - Update the plan reference between the `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` markers in `__CONTEXT_FILE__` to point to the plan file created in step 1 (the IMPL_PLAN path)
 
-**Output**: data-model.md, /contracts/*, quickstart.md, agent-specific file
+**Output**: data-model.md, /contracts/*, quickstart.md, updated agent context file
 
 ## Key rules
 
-- Use absolute paths
+- Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
 - ERROR on gate failures or unresolved clarifications

tests/integrations/test_cli.py

@@ -56,14 +56,19 @@ class TestInitIntegrationFlag:
 
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "copilot"
-        assert "scripts" in data
-        assert "update-context" in data["scripts"]
 
         opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
         assert opts["integration"] == "copilot"
+        assert opts["context_file"] == ".github/copilot-instructions.md"
 
         assert (project / ".specify" / "integrations" / "copilot.manifest.json").exists()
-        assert (project / ".specify" / "integrations" / "copilot" / "scripts" / "update-context.sh").exists()
+
+        # Context section should be upserted into the copilot instructions file
+        ctx_file = project / ".github" / "copilot-instructions.md"
+        assert ctx_file.exists()
+        ctx_content = ctx_file.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in ctx_content
+        assert "<!-- SPECKIT END -->" in ctx_content
 
         shared_manifest = project / ".specify" / "integrations" / "speckit.manifest.json"
         assert shared_manifest.exists()

tests/integrations/test_integration_base_markdown.py

@@ -99,7 +99,23 @@ class MarkdownIntegrationTests:
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
             assert "\nscripts:\n" not in content, f"{f.name} has unstripped scripts: block"
-            assert "\nagent_scripts:\n" not in content, f"{f.name} has unstripped agent_scripts: block"
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
 
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
@@ -132,30 +148,35 @@ class MarkdownIntegrationTests:
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
 
-    def test_sh_script_is_executable(self, tmp_path):
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = tmp_path / ".specify" / "integrations" / self.KEY / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            # Add user content around the section
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -203,6 +224,30 @@ class MarkdownIntegrationTests:
         commands = sorted(cmd_dir.glob("speckit.*"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -220,10 +265,6 @@ class MarkdownIntegrationTests:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.md")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(f".specify/integration.json")
         files.append(f".specify/init-options.json")
@@ -232,14 +273,14 @@ class MarkdownIntegrationTests:
 
         if script_variant == "sh":
             for name in ["check-prerequisites.sh", "common.sh", "create-new-feature.sh",
-                         "setup-plan.sh", "update-agent-context.sh"]:
+                         "setup-plan.sh"]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
             for name in ["check-prerequisites.ps1", "common.ps1", "create-new-feature.ps1",
-                         "setup-plan.ps1", "update-agent-context.ps1"]:
+                         "setup-plan.ps1"]:
                 files.append(f".specify/scripts/powershell/{name}")
 
-        for name in ["agent-file-template.md", "checklist-template.md",
+        for name in ["checklist-template.md",
                      "constitution-template.md", "plan-template.md",
                      "spec-template.md", "tasks-template.md"]:
             files.append(f".specify/templates/{name}")
@@ -248,6 +289,11 @@ class MarkdownIntegrationTests:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):

tests/integrations/test_integration_base_skills.py

@@ -173,6 +173,23 @@ class SkillsIntegrationTests:
             body = parts[2].strip() if len(parts) >= 3 else ""
             assert len(body) > 0, f"{f} has empty body"
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan skill must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.skills_dest(tmp_path) / "speckit-plan" / "SKILL.md"
+        assert plan_file.exists(), f"Plan skill {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan skill should reference {i.context_file!r} but it was not found"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            "Plan skill has unprocessed __CONTEXT_FILE__ placeholder"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -217,30 +234,34 @@ class SkillsIntegrationTests:
 
         assert (foreign_dir / "SKILL.md").exists(), "Foreign skill was removed"
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
 
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        sh = tmp_path / ".specify" / "integrations" / self.KEY / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -286,6 +307,30 @@ class SkillsIntegrationTests:
         skills_dir = i.skills_dest(project)
         assert skills_dir.is_dir(), f"Skills directory {skills_dir} not created"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- IntegrationOption ------------------------------------------------
 
     def test_options_include_skills_flag(self):
@@ -316,8 +361,6 @@ class SkillsIntegrationTests:
             ".specify/init-options.json",
             ".specify/integration.json",
             f".specify/integrations/{self.KEY}.manifest.json",
-            f".specify/integrations/{self.KEY}/scripts/update-context.ps1",
-            f".specify/integrations/{self.KEY}/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
         ]
@@ -328,7 +371,6 @@ class SkillsIntegrationTests:
                 ".specify/scripts/bash/common.sh",
                 ".specify/scripts/bash/create-new-feature.sh",
                 ".specify/scripts/bash/setup-plan.sh",
-                ".specify/scripts/bash/update-agent-context.sh",
             ]
         else:
             files += [
@@ -336,11 +378,9 @@ class SkillsIntegrationTests:
                 ".specify/scripts/powershell/common.ps1",
                 ".specify/scripts/powershell/create-new-feature.ps1",
                 ".specify/scripts/powershell/setup-plan.ps1",
-                ".specify/scripts/powershell/update-agent-context.ps1",
             ]
         # Templates
         files += [
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -352,6 +392,9 @@ class SkillsIntegrationTests:
             ".specify/workflows/speckit/workflow.yml",
             ".specify/workflows/workflow-registry.json",
         ]
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):

tests/integrations/test_integration_base_toml.py

@@ -310,6 +310,23 @@ class TomlIntegrationTests:
                 raise AssertionError(f"{f.name} is not valid TOML: {exc}") from exc
             assert "prompt" in parsed, f"{f.name} parsed TOML has no 'prompt' key"
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -341,37 +358,34 @@ class TomlIntegrationTests:
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
 
-    def test_sh_script_is_executable(self, tmp_path):
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = (
-            tmp_path
-            / ".specify"
-            / "integrations"
-            / self.KEY
-            / "scripts"
-            / "update-context.sh"
-        )
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -441,6 +455,30 @@ class TomlIntegrationTests:
         commands = sorted(cmd_dir.glob("speckit.*.toml"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -465,10 +503,6 @@ class TomlIntegrationTests:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.toml")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(".specify/integration.json")
         files.append(".specify/init-options.json")
@@ -481,7 +515,6 @@ class TomlIntegrationTests:
                 "common.sh",
                 "create-new-feature.sh",
                 "setup-plan.sh",
-                "update-agent-context.sh",
             ]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
@@ -490,12 +523,10 @@ class TomlIntegrationTests:
                 "common.ps1",
                 "create-new-feature.ps1",
                 "setup-plan.ps1",
-                "update-agent-context.ps1",
             ]:
                 files.append(f".specify/scripts/powershell/{name}")
 
         for name in [
-            "agent-file-template.md",
             "checklist-template.md",
             "constitution-template.md",
             "plan-template.md",
@@ -508,6 +539,11 @@ class TomlIntegrationTests:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):

tests/integrations/test_integration_base_yaml.py

@@ -189,6 +189,23 @@ class YamlIntegrationTests:
         assert "scripts:" not in parsed["prompt"]
         assert "---" not in parsed["prompt"]
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -220,37 +237,34 @@ class YamlIntegrationTests:
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
 
-    def test_sh_script_is_executable(self, tmp_path):
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = (
-            tmp_path
-            / ".specify"
-            / "integrations"
-            / self.KEY
-            / "scripts"
-            / "update-context.sh"
-        )
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -320,6 +334,30 @@ class YamlIntegrationTests:
         commands = sorted(cmd_dir.glob("speckit.*.yaml"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -344,10 +382,6 @@ class YamlIntegrationTests:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.yaml")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(".specify/integration.json")
         files.append(".specify/init-options.json")
@@ -360,7 +394,6 @@ class YamlIntegrationTests:
                 "common.sh",
                 "create-new-feature.sh",
                 "setup-plan.sh",
-                "update-agent-context.sh",
             ]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
@@ -369,12 +402,10 @@ class YamlIntegrationTests:
                 "common.ps1",
                 "create-new-feature.ps1",
                 "setup-plan.ps1",
-                "update-agent-context.ps1",
             ]:
                 files.append(f".specify/scripts/powershell/{name}")
 
         for name in [
-            "agent-file-template.md",
             "checklist-template.md",
             "constitution-template.md",
             "plan-template.md",
@@ -387,6 +418,11 @@ class YamlIntegrationTests:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):

tests/integrations/test_integration_catalog.py

@@ -285,7 +285,7 @@ VALID_DESCRIPTOR = {
         "commands": [
             {"name": "speckit.specify", "file": "templates/speckit.specify.md"},
         ],
-        "scripts": ["update-context.sh"],
+        "scripts": [],
     },
 }
 
@@ -305,7 +305,7 @@ class TestIntegrationDescriptor:
         assert desc.description == "Integration for My Agent"
         assert desc.requires_speckit_version == ">=0.6.0"
         assert len(desc.commands) == 1
-        assert desc.scripts == ["update-context.sh"]
+        assert desc.scripts == []
 
     def test_missing_schema_version(self, tmp_path):
         data = {**VALID_DESCRIPTOR}

tests/integrations/test_integration_claude.py

@@ -62,19 +62,17 @@ class TestClaudeIntegration:
         assert parsed["disable-model-invocation"] is False
         assert parsed["metadata"]["source"] == "templates/commands/plan.md"
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         integration = get_integration("claude")
         manifest = IntegrationManifest("claude", tmp_path)
-        created = integration.setup(tmp_path, manifest, script_type="sh")
+        integration.setup(tmp_path, manifest, script_type="sh")
 
-        scripts_dir = tmp_path / ".specify" / "integrations" / "claude" / "scripts"
-        assert scripts_dir.is_dir()
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-        tracked = {path.resolve().relative_to(tmp_path.resolve()).as_posix() for path in created}
-        assert ".specify/integrations/claude/scripts/update-context.sh" in tracked
-        assert ".specify/integrations/claude/scripts/update-context.ps1" in tracked
+        ctx_path = tmp_path / integration.context_file
+        assert ctx_path.exists()
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "<!-- SPECKIT END -->" in content
+        assert "read the current plan" in content
 
     def test_ai_flag_auto_promotes_and_enables_skills(self, tmp_path):
         from typer.testing import CliRunner

tests/integrations/test_integration_copilot.py

@@ -143,7 +143,20 @@ class TestCopilotIntegration:
             assert "__AGENT__" not in content, f"{agent_file.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{agent_file.name} has unprocessed {{ARGS}}"
             assert "\nscripts:\n" not in content
-            assert "\nagent_scripts:\n" not in content
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference copilot's context file."""
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        copilot.setup(tmp_path, m)
+        plan_file = tmp_path / ".github" / "agents" / "speckit.plan.agent.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert copilot.context_file in content, (
+            f"Plan command should reference {copilot.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     def test_complete_file_inventory_sh(self, tmp_path):
         """Every file produced by specify init --integration copilot --script sh."""
@@ -181,18 +194,15 @@ class TestCopilotIntegration:
             ".github/prompts/speckit.tasks.prompt.md",
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
+            ".github/copilot-instructions.md",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
             ".specify/integrations/speckit.manifest.json",
-            ".specify/integrations/copilot/scripts/update-context.ps1",
-            ".specify/integrations/copilot/scripts/update-context.sh",
             ".specify/scripts/bash/check-prerequisites.sh",
             ".specify/scripts/bash/common.sh",
             ".specify/scripts/bash/create-new-feature.sh",
             ".specify/scripts/bash/setup-plan.sh",
-            ".specify/scripts/bash/update-agent-context.sh",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -243,18 +253,15 @@ class TestCopilotIntegration:
             ".github/prompts/speckit.tasks.prompt.md",
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
+            ".github/copilot-instructions.md",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
             ".specify/integrations/speckit.manifest.json",
-            ".specify/integrations/copilot/scripts/update-context.ps1",
-            ".specify/integrations/copilot/scripts/update-context.sh",
             ".specify/scripts/powershell/check-prerequisites.ps1",
             ".specify/scripts/powershell/common.ps1",
             ".specify/scripts/powershell/create-new-feature.ps1",
             ".specify/scripts/powershell/setup-plan.ps1",
-            ".specify/scripts/powershell/update-agent-context.ps1",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",

tests/integrations/test_integration_cursor_agent.py

@@ -1,5 +1,10 @@
 """Tests for CursorAgentIntegration."""
 
+from pathlib import Path
+
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.manifest import IntegrationManifest
+
 from .test_integration_base_skills import SkillsIntegrationTests
 
 
@@ -11,6 +16,81 @@ class TestCursorAgentIntegration(SkillsIntegrationTests):
     CONTEXT_FILE = ".cursor/rules/specify-rules.mdc"
 
 
+class TestCursorMdcFrontmatter:
+    """Verify .mdc frontmatter handling in upsert/remove context section."""
+
+    def _setup(self, tmp_path: Path):
+        i = get_integration("cursor-agent")
+        m = IntegrationManifest("cursor-agent", tmp_path)
+        return i, m
+
+    def test_new_mdc_gets_frontmatter(self, tmp_path):
+        """A freshly created .mdc file includes alwaysApply: true."""
+        i, m = self._setup(tmp_path)
+        i.setup(tmp_path, m)
+        ctx = (tmp_path / i.context_file).read_text(encoding="utf-8")
+        assert ctx.startswith("---\n")
+        assert "alwaysApply: true" in ctx
+
+    def test_existing_mdc_without_frontmatter_gets_it(self, tmp_path):
+        """An existing .mdc without frontmatter gets it added."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text("# User rules\n", encoding="utf-8")
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert content.lstrip().startswith("---")
+        assert "alwaysApply: true" in content
+        assert "# User rules" in content
+
+    def test_existing_mdc_with_frontmatter_preserves_it(self, tmp_path):
+        """An existing .mdc with custom frontmatter is preserved."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text(
+            "---\nalwaysApply: true\ncustomKey: hello\n---\n\n# Rules\n",
+            encoding="utf-8",
+        )
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "alwaysApply: true" in content
+        assert "customKey: hello" in content
+        assert "<!-- SPECKIT START -->" in content
+
+    def test_existing_mdc_wrong_alwaysapply_fixed(self, tmp_path):
+        """An .mdc with alwaysApply: false gets corrected."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text(
+            "---\nalwaysApply: false\n---\n\n# Rules\n",
+            encoding="utf-8",
+        )
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "alwaysApply: true" in content
+        assert "alwaysApply: false" not in content
+
+    def test_upsert_idempotent_no_duplicate_frontmatter(self, tmp_path):
+        """Repeated upserts don't duplicate frontmatter."""
+        i, m = self._setup(tmp_path)
+        i.upsert_context_section(tmp_path)
+        i.upsert_context_section(tmp_path)
+        content = (tmp_path / i.context_file).read_text(encoding="utf-8")
+        assert content.count("alwaysApply") == 1
+
+    def test_remove_deletes_mdc_with_only_frontmatter(self, tmp_path):
+        """Removing the section from a Speckit-only .mdc deletes the file."""
+        i, m = self._setup(tmp_path)
+        i.upsert_context_section(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        assert ctx_path.exists()
+        i.remove_context_section(tmp_path)
+        assert not ctx_path.exists()
+
+
 class TestCursorAgentAutoPromote:
     """--ai cursor-agent auto-promotes to integration path."""
 

tests/integrations/test_integration_forge.py

@@ -73,19 +73,16 @@ class TestForgeIntegration:
         for f in command_files:
             assert f.name.endswith(".md")
 
-    def test_setup_installs_update_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         from specify_cli.integrations.forge import ForgeIntegration
         forge = ForgeIntegration()
         m = IntegrationManifest("forge", tmp_path)
-        created = forge.setup(tmp_path, m)
-        script_files = [f for f in created if "scripts" in f.parts]
-        assert len(script_files) > 0
-        sh_script = tmp_path / ".specify" / "integrations" / "forge" / "scripts" / "update-context.sh"
-        ps_script = tmp_path / ".specify" / "integrations" / "forge" / "scripts" / "update-context.ps1"
-        assert sh_script in created
-        assert ps_script in created
-        assert sh_script.exists()
-        assert ps_script.exists()
+        forge.setup(tmp_path, m)
+        ctx_path = tmp_path / forge.context_file
+        assert ctx_path.exists()
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "<!-- SPECKIT END -->" in content
 
     def test_all_created_files_tracked_in_manifest(self, tmp_path):
         from specify_cli.integrations.forge import ForgeIntegration
@@ -159,7 +156,20 @@ class TestForgeIntegration:
             assert "$ARGUMENTS" not in content, f"{cmd_file.name} has unprocessed $ARGUMENTS"
             # Frontmatter sections should be stripped
             assert "\nscripts:\n" not in content
-            assert "\nagent_scripts:\n" not in content
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference forge's context file."""
+        from specify_cli.integrations.forge import ForgeIntegration
+        forge = ForgeIntegration()
+        m = IntegrationManifest("forge", tmp_path)
+        forge.setup(tmp_path, m)
+        plan_file = tmp_path / ".forge" / "commands" / "speckit.plan.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert forge.context_file in content, (
+            f"Plan command should reference {forge.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     def test_forge_specific_transformations(self, tmp_path):
         """Test Forge-specific processing: name injection and handoffs stripping."""

tests/integrations/test_integration_generic.py

@@ -31,9 +31,9 @@ class TestGenericIntegration:
         i = get_integration("generic")
         assert i.config["requires_cli"] is False
 
-    def test_context_file_is_none(self):
+    def test_context_file_is_agents_md(self):
         i = get_integration("generic")
-        assert i.context_file is None
+        assert i.context_file == "AGENTS.md"
 
     # -- Options ----------------------------------------------------------
 
@@ -158,30 +158,31 @@ class TestGenericIntegration:
             cmd_files = [f for f in created if "scripts" not in f.parts]
             assert len(cmd_files) > 0
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration("generic")
         m = IntegrationManifest("generic", tmp_path)
         i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        scripts_dir = tmp_path / ".specify" / "integrations" / "generic" / "scripts"
-        assert scripts_dir.is_dir(), "Scripts directory not created for generic"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists()
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
 
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference generic's context file."""
         i = get_integration("generic")
         m = IntegrationManifest("generic", tmp_path)
         i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
-        i = get_integration("generic")
-        m = IntegrationManifest("generic", tmp_path)
-        i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        sh = tmp_path / ".specify" / "integrations" / "generic" / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        plan_file = tmp_path / ".custom" / "cmds" / "speckit.plan.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     # -- CLI --------------------------------------------------------------
 
@@ -198,6 +199,28 @@ class TestGenericIntegration:
         # The integration path validates via setup()
         assert result.exit_code != 0
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the generic integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "opts-generic"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "generic",
+                "--ai-commands-dir", ".myagent/commands",
+                "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        assert opts.get("context_file") == "AGENTS.md"
+
     def test_complete_file_inventory_sh(self, tmp_path):
         """Every file produced by specify init --integration generic --ai-commands-dir ... --script sh."""
         from typer.testing import CliRunner
@@ -221,6 +244,7 @@ class TestGenericIntegration:
             for p in project.rglob("*") if p.is_file()
         )
         expected = sorted([
+            "AGENTS.md",
             ".myagent/commands/speckit.analyze.md",
             ".myagent/commands/speckit.checklist.md",
             ".myagent/commands/speckit.clarify.md",
@@ -233,16 +257,12 @@ class TestGenericIntegration:
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",
-            ".specify/integrations/generic/scripts/update-context.ps1",
-            ".specify/integrations/generic/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
             ".specify/scripts/bash/check-prerequisites.sh",
             ".specify/scripts/bash/common.sh",
             ".specify/scripts/bash/create-new-feature.sh",
             ".specify/scripts/bash/setup-plan.sh",
-            ".specify/scripts/bash/update-agent-context.sh",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -279,6 +299,7 @@ class TestGenericIntegration:
             for p in project.rglob("*") if p.is_file()
         )
         expected = sorted([
+            "AGENTS.md",
             ".myagent/commands/speckit.analyze.md",
             ".myagent/commands/speckit.checklist.md",
             ".myagent/commands/speckit.clarify.md",
@@ -291,16 +312,12 @@ class TestGenericIntegration:
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",
-            ".specify/integrations/generic/scripts/update-context.ps1",
-            ".specify/integrations/generic/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
             ".specify/scripts/powershell/check-prerequisites.ps1",
             ".specify/scripts/powershell/common.ps1",
             ".specify/scripts/powershell/create-new-feature.ps1",
             ".specify/scripts/powershell/setup-plan.ps1",
-            ".specify/scripts/powershell/update-agent-context.ps1",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",

tests/test_agent_config_consistency.py

@@ -1,6 +1,5 @@
 """Consistency checks for agent configuration across runtime surfaces."""
 
-import re
 from pathlib import Path
 
 from specify_cli import AGENT_CONFIG, AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP
@@ -61,20 +60,6 @@ class TestAgentConfigConsistency:
         assert "sha256sum -c -" in post_create_text
         assert "KIRO_SKIP_KIRO_INSTALLER_VERIFY" not in post_create_text
 
-    def test_agent_context_scripts_use_kiro_cli(self):
-        """Agent context scripts should advertise kiro-cli and not legacy q agent key."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "kiro-cli" in bash_text
-        assert "kiro-cli" in pwsh_text
-        assert "Amazon Q Developer CLI" not in bash_text
-        assert "Amazon Q Developer CLI" not in pwsh_text
-
     # --- Tabnine CLI consistency checks ---
 
     def test_runtime_config_includes_tabnine(self):
@@ -96,20 +81,6 @@ class TestAgentConfigConsistency:
         assert cfg["args"] == "{{args}}"
         assert cfg["extension"] == ".toml"
 
-    def test_agent_context_scripts_include_tabnine(self):
-        """Agent context scripts should support tabnine agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "tabnine" in bash_text
-        assert "TABNINE_FILE" in bash_text
-        assert "tabnine" in pwsh_text
-        assert "TABNINE_FILE" in pwsh_text
-
     def test_ai_help_includes_tabnine(self):
         """CLI help text for --ai should include tabnine."""
         assert "tabnine" in AI_ASSISTANT_HELP
@@ -132,18 +103,6 @@ class TestAgentConfigConsistency:
         assert kimi_cfg["dir"] == ".kimi/skills"
         assert kimi_cfg["extension"] == "/SKILL.md"
 
-    def test_kimi_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'kimi' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "kimi" in validate_set_values
-
     def test_ai_help_includes_kimi(self):
         """CLI help text for --ai should include kimi."""
         assert "kimi" in AI_ASSISTANT_HELP
@@ -168,32 +127,6 @@ class TestAgentConfigConsistency:
         assert trae_cfg["args"] == "$ARGUMENTS"
         assert trae_cfg["extension"] == "/SKILL.md"
 
-    def test_trae_in_agent_context_scripts(self):
-        """Agent context scripts should support trae agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "trae" in bash_text
-        assert "TRAE_FILE" in bash_text
-        assert "trae" in pwsh_text
-        assert "TRAE_FILE" in pwsh_text
-
-    def test_trae_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'trae' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "trae" in validate_set_values
-
     def test_ai_help_includes_trae(self):
         """CLI help text for --ai should include trae."""
         assert "trae" in AI_ASSISTANT_HELP
@@ -219,32 +152,6 @@ class TestAgentConfigConsistency:
         assert pi_cfg["args"] == "$ARGUMENTS"
         assert pi_cfg["extension"] == ".md"
 
-    def test_pi_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'pi' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "pi" in validate_set_values
-
-    def test_agent_context_scripts_include_pi(self):
-        """Agent context scripts should support pi agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "pi" in bash_text
-        assert "Pi Coding Agent" in bash_text
-        assert "pi" in pwsh_text
-        assert "Pi Coding Agent" in pwsh_text
-
     def test_ai_help_includes_pi(self):
         """CLI help text for --ai should include pi."""
         assert "pi" in AI_ASSISTANT_HELP
@@ -267,20 +174,6 @@ class TestAgentConfigConsistency:
         assert cfg["iflow"]["format"] == "markdown"
         assert cfg["iflow"]["args"] == "$ARGUMENTS"
 
-    def test_iflow_in_agent_context_scripts(self):
-        """Agent context scripts should support iflow agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "iflow" in bash_text
-        assert "IFLOW_FILE" in bash_text
-        assert "iflow" in pwsh_text
-        assert "IFLOW_FILE" in pwsh_text
-
     def test_ai_help_includes_iflow(self):
         """CLI help text for --ai should include iflow."""
         assert "iflow" in AI_ASSISTANT_HELP
@@ -303,18 +196,6 @@ class TestAgentConfigConsistency:
         assert cfg["goose"]["format"] == "yaml"
         assert cfg["goose"]["args"] == "{{args}}"
 
-    def test_goose_in_agent_context_scripts(self):
-        """Agent context scripts should support goose agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "goose" in bash_text
-        assert "goose" in pwsh_text
-
     def test_ai_help_includes_goose(self):
         """CLI help text for --ai should include goose."""
         assert "goose" in AI_ASSISTANT_HELP

tests/test_cursor_frontmatter.py

@@ -1,266 +0,0 @@
-"""
-Tests for Cursor .mdc frontmatter generation (issue #669).
-
-Verifies that update-agent-context.sh properly prepends YAML frontmatter
-to .mdc files so that Cursor IDE auto-includes the rules.
-"""
-
-import os
-import shutil
-import subprocess
-import textwrap
-
-import pytest
-
-from tests.conftest import requires_bash
-
-SCRIPT_PATH = os.path.join(
-    os.path.dirname(__file__),
-    os.pardir,
-    "scripts",
-    "bash",
-    "update-agent-context.sh",
-)
-
-EXPECTED_FRONTMATTER_LINES = [
-    "---",
-    "description: Project Development Guidelines",
-    'globs: ["**/*"]',
-    "alwaysApply: true",
-    "---",
-]
-
-requires_git = pytest.mark.skipif(
-    shutil.which("git") is None,
-    reason="git is not installed",
-)
-
-
-class TestScriptFrontmatterPattern:
-    """Static analysis — no git required."""
-
-    def test_create_new_has_mdc_frontmatter_logic(self):
-        """create_new_agent_file() must contain .mdc frontmatter logic."""
-        with open(SCRIPT_PATH, encoding="utf-8") as f:
-            content = f.read()
-        assert 'if [[ "$target_file" == *.mdc ]]' in content
-        assert "alwaysApply: true" in content
-
-    def test_update_existing_has_mdc_frontmatter_logic(self):
-        """update_existing_agent_file() must also handle .mdc frontmatter."""
-        with open(SCRIPT_PATH, encoding="utf-8") as f:
-            content = f.read()
-        # There should be two occurrences of the .mdc check — one per function
-        occurrences = content.count('if [[ "$target_file" == *.mdc ]]')
-        assert occurrences >= 2, (
-            f"Expected at least 2 .mdc frontmatter checks, found {occurrences}"
-        )
-
-    def test_powershell_script_has_mdc_frontmatter_logic(self):
-        """PowerShell script must also handle .mdc frontmatter."""
-        ps_path = os.path.join(
-            os.path.dirname(__file__),
-            os.pardir,
-            "scripts",
-            "powershell",
-            "update-agent-context.ps1",
-        )
-        with open(ps_path, encoding="utf-8") as f:
-            content = f.read()
-        assert "alwaysApply: true" in content
-        occurrences = content.count(r"\.mdc$")
-        assert occurrences >= 2, (
-            f"Expected at least 2 .mdc frontmatter checks in PS script, found {occurrences}"
-        )
-
-
-@requires_git
-@requires_bash
-class TestCursorFrontmatterIntegration:
-    """Integration tests using a real git repo."""
-
-    @pytest.fixture
-    def git_repo(self, tmp_path):
-        """Create a minimal git repo with the spec-kit structure."""
-        repo = tmp_path / "repo"
-        repo.mkdir()
-
-        # Init git repo
-        subprocess.run(
-            ["git", "init"], cwd=str(repo), capture_output=True, check=True
-        )
-        subprocess.run(
-            ["git", "config", "user.email", "test@test.com"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create .specify dir with config
-        specify_dir = repo / ".specify"
-        specify_dir.mkdir()
-        (specify_dir / "config.yaml").write_text(
-            textwrap.dedent("""\
-                project_type: webapp
-                language: python
-                framework: fastapi
-                database: N/A
-            """)
-        )
-
-        # Create template
-        templates_dir = specify_dir / "templates"
-        templates_dir.mkdir()
-        (templates_dir / "agent-file-template.md").write_text(
-            "# [PROJECT NAME] Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: [DATE]\n\n"
-            "## Active Technologies\n\n"
-            "[EXTRACTED FROM ALL PLAN.MD FILES]\n\n"
-            "## Project Structure\n\n"
-            "[ACTUAL STRUCTURE FROM PLANS]\n\n"
-            "## Development Commands\n\n"
-            "[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES]\n\n"
-            "## Coding Conventions\n\n"
-            "[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE]\n\n"
-            "## Recent Changes\n\n"
-            "[LAST 3 FEATURES AND WHAT THEY ADDED]\n"
-        )
-
-        # Create initial commit
-        subprocess.run(
-            ["git", "add", "-A"], cwd=str(repo), capture_output=True, check=True
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "init"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create a feature branch so CURRENT_BRANCH detection works
-        subprocess.run(
-            ["git", "checkout", "-b", "001-test-feature"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create a spec so the script detects the feature
-        spec_dir = repo / "specs" / "001-test-feature"
-        spec_dir.mkdir(parents=True)
-        (spec_dir / "plan.md").write_text(
-            "# Test Feature Plan\n\n"
-            "## Technology Stack\n\n"
-            "- Language: Python\n"
-            "- Framework: FastAPI\n"
-        )
-
-        return repo
-
-    def _run_update(self, repo, agent_type="cursor-agent"):
-        """Run update-agent-context.sh for a specific agent type."""
-        script = os.path.abspath(SCRIPT_PATH)
-        result = subprocess.run(
-            ["bash", script, agent_type],
-            cwd=str(repo),
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-        return result
-
-    def test_new_mdc_file_has_frontmatter(self, git_repo):
-        """Creating a new .mdc file must include YAML frontmatter."""
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        mdc_file = git_repo / ".cursor" / "rules" / "specify-rules.mdc"
-        assert mdc_file.exists(), "Cursor .mdc file was not created"
-
-        content = mdc_file.read_text()
-        lines = content.splitlines()
-
-        # First line must be the opening ---
-        assert lines[0] == "---", f"Expected frontmatter start, got: {lines[0]}"
-
-        # Check all frontmatter lines are present
-        for expected in EXPECTED_FRONTMATTER_LINES:
-            assert expected in content, f"Missing frontmatter line: {expected}"
-
-        # Content after frontmatter should be the template content
-        assert "Development Guidelines" in content
-
-    def test_existing_mdc_without_frontmatter_gets_it_added(self, git_repo):
-        """Updating an existing .mdc file that lacks frontmatter must add it."""
-        # First, create the file WITHOUT frontmatter (simulating pre-fix state)
-        cursor_dir = git_repo / ".cursor" / "rules"
-        cursor_dir.mkdir(parents=True, exist_ok=True)
-        mdc_file = cursor_dir / "specify-rules.mdc"
-        mdc_file.write_text(
-            "# repo Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: 2025-01-01\n\n"
-            "## Active Technologies\n\n"
-            "- Python + FastAPI (main)\n\n"
-            "## Recent Changes\n\n"
-            "- main: Added Python + FastAPI\n"
-        )
-
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        content = mdc_file.read_text()
-        lines = content.splitlines()
-
-        assert lines[0] == "---", f"Expected frontmatter start, got: {lines[0]}"
-        for expected in EXPECTED_FRONTMATTER_LINES:
-            assert expected in content, f"Missing frontmatter line: {expected}"
-
-    def test_existing_mdc_with_frontmatter_not_duplicated(self, git_repo):
-        """Updating an .mdc file that already has frontmatter must not duplicate it."""
-        cursor_dir = git_repo / ".cursor" / "rules"
-        cursor_dir.mkdir(parents=True, exist_ok=True)
-        mdc_file = cursor_dir / "specify-rules.mdc"
-
-        frontmatter = (
-            "---\n"
-            "description: Project Development Guidelines\n"
-            'globs: ["**/*"]\n'
-            "alwaysApply: true\n"
-            "---\n\n"
-        )
-        body = (
-            "# repo Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: 2025-01-01\n\n"
-            "## Active Technologies\n\n"
-            "- Python + FastAPI (main)\n\n"
-            "## Recent Changes\n\n"
-            "- main: Added Python + FastAPI\n"
-        )
-        mdc_file.write_text(frontmatter + body)
-
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        content = mdc_file.read_text()
-        # Count occurrences of the frontmatter delimiter
-        assert content.count("alwaysApply: true") == 1, (
-            "Frontmatter was duplicated"
-        )
-
-    def test_non_mdc_file_has_no_frontmatter(self, git_repo):
-        """Non-.mdc agent files (e.g., Claude) must NOT get frontmatter."""
-        result = self._run_update(git_repo, agent_type="claude")
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        claude_file = git_repo / ".claude" / "CLAUDE.md"
-        if claude_file.exists():
-            content = claude_file.read_text()
-            assert not content.startswith("---"), (
-                "Non-mdc file should not have frontmatter"
-            )

tests/test_extension_skills.py

@@ -396,11 +396,8 @@ class TestExtensionSkillRegistration:
             "description: Scripted plan command\n"
             "scripts:\n"
             "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "agent_scripts:\n"
-            "  sh: ../../scripts/bash/update-agent-context.sh __AGENT__\n"
             "---\n\n"
             "Run {SCRIPT}\n"
-            "Then {AGENT_SCRIPT}\n"
             "Review templates/checklist.md and memory/constitution.md for __AGENT__.\n"
         )
 
@@ -409,11 +406,9 @@ class TestExtensionSkillRegistration:
 
         content = (skills_dir / "speckit-scripted-ext-plan" / "SKILL.md").read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         assert "{ARGS}" not in content
         assert "__AGENT__" not in content
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh claude" in content
         assert ".specify/templates/checklist.md" in content
         assert ".specify/memory/constitution.md" in content
 

tests/test_extensions.py

@@ -1334,13 +1334,9 @@ description: "Scripted command"
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 Agent __AGENT__
 """
         )
@@ -1361,11 +1357,9 @@ Agent __AGENT__
 
         content = skill_file.read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         assert "__AGENT__" not in content
         assert "{ARGS}" not in content
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
     def test_codex_skill_alias_frontmatter_matches_alias_name(self, project_dir, temp_dir):
         """Codex alias skills should render their own matching `name:` frontmatter."""
@@ -1451,13 +1445,9 @@ description: "Fallback scripted command"
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 """
         )
 
@@ -1474,13 +1464,10 @@ Then {AGENT_SCRIPT}
 
         content = skill_file.read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         if platform.system().lower().startswith("win"):
             assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
-            assert ".specify/scripts/powershell/update-agent-context.ps1 codex" in content
         else:
             assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-            assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
     def test_codex_skill_registration_handles_non_dict_init_options(
         self, project_dir, temp_dir
@@ -1577,13 +1564,9 @@ description: "Windows fallback scripted command"
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 """
         )
 
@@ -1599,7 +1582,6 @@ Then {AGENT_SCRIPT}
 
         content = skill_file.read_text()
         assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
-        assert ".specify/scripts/powershell/update-agent-context.ps1 -AgentType codex" in content
         assert ".specify/scripts/bash/setup-plan.sh" not in content
 
     def test_register_commands_for_copilot(self, extension_dir, project_dir):

tests/test_presets.py

@@ -1648,7 +1648,6 @@ CORE_TEMPLATE_NAMES = [
     "tasks-template",
     "checklist-template",
     "constitution-template",
-    "agent-file-template",
 ]
 
 
@@ -2911,7 +2910,7 @@ class TestLeanPreset:
             assert tmpl_path.exists(), f"Missing command file: {tmpl['file']}"
 
     def test_lean_commands_have_no_scripts(self):
-        """Verify lean commands have no scripts or agent_scripts in frontmatter."""
+        """Verify lean commands have no scripts in frontmatter."""
         from specify_cli.agents import CommandRegistrar
 
         for name in LEAN_COMMAND_NAMES:
@@ -2919,7 +2918,6 @@ class TestLeanPreset:
             content = cmd_path.read_text()
             frontmatter, _ = CommandRegistrar.parse_frontmatter(content)
             assert "scripts" not in frontmatter, f"{name} should not have scripts in frontmatter"
-            assert "agent_scripts" not in frontmatter, f"{name} should not have agent_scripts in frontmatter"
 
     def test_lean_commands_have_no_hooks(self):
         """Verify lean commands do not contain extension hook boilerplate."""