Files
github-spec-kit/templates/commands/clarify.md
Copilot 50da3a0f77 Extract agent context updates into bundled agent-context extension (#2546)
* Initial plan

* Extract agent context updates into bundled agent-context extension

* Potential fix for pull request finding 'Unused import'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* Potential fix for pull request finding 'Unused import'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* fix: address review comments on agent-context extension

- bash: parse init-options.json with a single python3 invocation instead
  of three separate read_json_field calls, for parity with the PowerShell
  ConvertFrom-Json approach and to avoid divergent error semantics
- bash: use parameter expansion to strip PROJECT_ROOT prefix from plan
  path instead of sed interpolation, avoiding special-character fragility
- powershell: limit Get-ChildItem to -Depth 1 so plan.md discovery matches
  the bash glob specs/*/plan.md (one level deep) — fixes cross-platform
  inconsistency with nested plan.md files
- powershell: replace Substring+Length relative-path with
  [System.IO.Path]::GetRelativePath for robustness across case/PSDrive
  differences
- __init__.py: move agent-context extension install to after
  save_init_options so init-options.json is present when hooks run
- __init__.py: seed context_markers in init-options only when
  context_file is truthy; avoids noise for integrations without a context
  file
- integrations/base.py: narrow blanket except Exception in
  _resolve_context_markers to ImportError / (OSError, ValueError) so
  unexpected bugs surface instead of being silently swallowed

* fix: gate context_markers in _update_init_options_for_integration on context_file

Apply the same gating logic used during `specify init`: only write
context_markers to init-options.json when the integration actually has a
context_file set.  When switching to an integration without a context file
the stale markers are removed, keeping the two init paths consistent.

* fix: move context_file/context_markers from init-options.json to agent-context extension config

* Potential fix for pull request finding 'Unused global variable'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* fix: clarify local import comment in agents.py

* Fix remaining agent-context review findings

* Fix follow-up agent-context review issues

* Address review feedback: narrow except, improve PyYAML messaging, surface config-written note

* Fix double-space in PyYAML install hint message

* Potential fix for pull request finding 'Empty except'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* Potential fix for pull request finding 'Empty except'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* Address latest agent-context review feedback

* Harden bash config parse output handling

* Clarify ImportError-only fallback comment

* Apply review feedback: drop dead try/except, guard ext-config creation, explicit ConvertFrom-Yaml check

* Remove redundant $Options = $null in PS1 catch block

* Add constitution directives, deprecation warning, agent-context auto-install, and init flow fix

- Add constitution-loading directive to specify, clarify, tasks, checklist, taskstoissues commands
- Add deprecation warning (v0.12.0) in upsert_context_section()
- Auto-install agent-context extension during specify init
- Move context_file from init-options.json to agent-context extension config
- Add tests: deprecation warning, corrupt config, constitution directives
- Update file inventories across all integration tests

* Address review: fix init ordering, test coverage, and hermes inventory

- Move agent-context extension install after init-options.json is saved
  so skill registration can read ai_skills + integration key
- Write extension config after install (avoids template overwriting context_file)
- Fix test_defaults_when_markers_field_missing to truly test missing markers key
- Update hermes tests to allow extension-installed agent-context skill

* Address review: chmod ordering, preserve markers, PS1 Python check, YAML key order

- Move ensure_executable_scripts after agent-context extension install
  so extension scripts get execute bits set
- Use preserve_markers=True on reinit to keep user-customized markers
- Add Python 3 version check in PowerShell fallback (matching bash behavior)
- Add sort_keys=False to yaml.safe_dump for stable config output

* Address review: path traversal guards and docstring fix

- Reject absolute paths and '..' segments in context_file in both bash and
  PowerShell scripts to prevent writes outside the project root
- Fix docstring in _update_init_options_for_integration to accurately
  describe marker preservation behavior

* Address review: strict enabled check, docstring, segment-level path traversal

- Use 'is not False' for enabled check so only literal False disables
- Update upsert_context_section docstring to mention disabled-extension return
- Fix path traversal guards to check actual path segments, not substrings
  (allows filenames like 'notes..md' while rejecting '../' traversal)

* Address review: UnicodeError handling, missing extension warning

- Add UnicodeError to exception tuples in _load_agent_context_config and
  _resolve_context_markers so garbled UTF-8 config files fall back to defaults
- Emit error (with reinstall command) instead of silent skip when bundled
  agent-context extension is not found during init

* Address review: bash backslash traversal guard, wheel packaging

- Reject backslash separators and Windows drive-letter paths in bash
  context_file validation (prevents traversal on Git-Bash/Windows)
- Add extensions/agent-context to pyproject.toml force-include so the
  bundled extension is included in wheel builds

* Address review: write extension config before init-options.json

- Reorder writes in _update_init_options_for_integration so the
  agent-context extension config is updated first; if it fails,
  init-options.json remains consistent with the previous state

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
2026-05-30 06:37:18 -05:00

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---
description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
handoffs:
- label: Build Technical Plan
agent: speckit.plan
prompt: Create a plan for the spec. I am building with...
scripts:
sh: scripts/bash/check-prerequisites.sh --json --paths-only
ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly
---
## User Input
```text
$ARGUMENTS
```
You **MUST** consider the user input before proceeding (if not empty).
## Pre-Execution Checks
**Check for extension hooks (before clarification)**:
- Check if `.specify/extensions.yml` exists in the project root.
- If it exists, read it and look for entries under the `hooks.before_clarify` key
- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
- If the hook has no `condition` field, or it is null/empty, treat the hook as executable
- If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
- For each executable hook, output the following based on its `optional` flag:
- **Optional hook** (`optional: true`):
```
## Extension Hooks
**Optional Pre-Hook**: {extension}
Command: `/{command}`
Description: {description}
Prompt: {prompt}
To execute: `/{command}`
```
- **Mandatory hook** (`optional: false`):
```
## Extension Hooks
**Automatic Pre-Hook**: {extension}
Executing: `/{command}`
EXECUTE_COMMAND: {command}
Wait for the result of the hook command before proceeding to the Outline.
```
- If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
## Outline
Goal: Detect and reduce ambiguity or missing decision points in the active feature specification and record the clarifications directly in the spec file.
Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `__SPECKIT_COMMAND_PLAN__`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.
Execution steps:
1. Run `{SCRIPT}` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
- `FEATURE_DIR`
- `FEATURE_SPEC`
- (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)
- If JSON parsing fails, abort and instruct user to re-run `__SPECKIT_COMMAND_SPECIFY__` or verify feature branch environment.
- For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
2. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
3. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
Functional Scope & Behavior:
- Core user goals & success criteria
- Explicit out-of-scope declarations
- User roles / personas differentiation
Domain & Data Model:
- Entities, attributes, relationships
- Identity & uniqueness rules
- Lifecycle/state transitions
- Data volume / scale assumptions
Interaction & UX Flow:
- Critical user journeys / sequences
- Error/empty/loading states
- Accessibility or localization notes
Non-Functional Quality Attributes:
- Performance (latency, throughput targets)
- Scalability (horizontal/vertical, limits)
- Reliability & availability (uptime, recovery expectations)
- Observability (logging, metrics, tracing signals)
- Security & privacy (authN/Z, data protection, threat assumptions)
- Compliance / regulatory constraints (if any)
Integration & External Dependencies:
- External services/APIs and failure modes
- Data import/export formats
- Protocol/versioning assumptions
Edge Cases & Failure Handling:
- Negative scenarios
- Rate limiting / throttling
- Conflict resolution (e.g., concurrent edits)
Constraints & Tradeoffs:
- Technical constraints (language, storage, hosting)
- Explicit tradeoffs or rejected alternatives
Terminology & Consistency:
- Canonical glossary terms
- Avoided synonyms / deprecated terms
Completion Signals:
- Acceptance criteria testability
- Measurable Definition of Done style indicators
Misc / Placeholders:
- TODO markers / unresolved decisions
- Ambiguous adjectives ("robust", "intuitive") lacking quantification
For each category with Partial or Missing status, add a candidate question opportunity unless:
- Clarification would not materially change implementation or validation strategy
- Information is better deferred to planning phase (note internally)
4. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
- Maximum of 5 total questions across the whole session.
- Each question must be answerable with EITHER:
- A short multiplechoice selection (25 distinct, mutually exclusive options), OR
- A one-word / shortphrase answer (explicitly constrain: "Answer in <=5 words").
- Only include questions whose answers materially impact architecture, data modeling, task decomposition, test design, UX behavior, operational readiness, or compliance validation.
- Ensure category coverage balance: attempt to cover the highest impact unresolved categories first; avoid asking two low-impact questions when a single high-impact area (e.g., security posture) is unresolved.
- Exclude questions already answered, trivial stylistic preferences, or plan-level execution details (unless blocking correctness).
- Favor clarifications that reduce downstream rework risk or prevent misaligned acceptance tests.
- If more than 5 categories remain unresolved, select the top 5 by (Impact * Uncertainty) heuristic.
5. Sequential questioning loop (interactive):
- Present EXACTLY ONE question at a time.
- For multiplechoice questions:
- **Analyze all options** and determine the **most suitable option** based on:
- Best practices for the project type
- Common patterns in similar implementations
- Risk reduction (security, performance, maintainability)
- Alignment with any explicit project goals or constraints visible in the spec
- Present your **recommended option prominently** at the top with clear reasoning (1-2 sentences explaining why this is the best choice).
- Format as: `**Recommended:** Option [X] - <reasoning>`
- Then render all options as a Markdown table:
| Option | Description |
|--------|-------------|
| A | <Option A description> |
| B | <Option B description> |
| C | <Option C description> (add D/E as needed up to 5) |
| Short | Provide a different short answer (<=5 words) (Include only if free-form alternative is appropriate) |
- After the table, add: `You can reply with the option letter (e.g., "A"), accept the recommendation by saying "yes" or "recommended", or provide your own short answer.`
- For shortanswer style (no meaningful discrete options):
- Provide your **suggested answer** based on best practices and context.
- Format as: `**Suggested:** <your proposed answer> - <brief reasoning>`
- Then output: `Format: Short answer (<=5 words). You can accept the suggestion by saying "yes" or "suggested", or provide your own answer.`
- After the user answers:
- If the user replies with "yes", "recommended", or "suggested", use your previously stated recommendation/suggestion as the answer.
- Otherwise, validate the answer maps to one option or fits the <=5 word constraint.
- If ambiguous, ask for a quick disambiguation (count still belongs to same question; do not advance).
- Once satisfactory, record it in working memory (do not yet write to disk) and move to the next queued question.
- Stop asking further questions when:
- All critical ambiguities resolved early (remaining queued items become unnecessary), OR
- User signals completion ("done", "good", "no more"), OR
- You reach 5 asked questions.
- Never reveal future queued questions in advance.
- If no valid questions exist at start, immediately report no critical ambiguities.
6. Integration after EACH accepted answer (incremental update approach):
- Maintain in-memory representation of the spec (loaded once at start) plus the raw file contents.
- For the first integrated answer in this session:
- Ensure a `## Clarifications` section exists (create it just after the highest-level contextual/overview section per the spec template if missing).
- Under it, create (if not present) a `### Session YYYY-MM-DD` subheading for today.
- Append a bullet line immediately after acceptance: `- Q: <question> → A: <final answer>`.
- Then immediately apply the clarification to the most appropriate section(s):
- Functional ambiguity → Update or add a bullet in Functional Requirements.
- User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
- Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
- Non-functional constraint → Add/modify measurable criteria in Success Criteria > Measurable Outcomes (convert vague adjective to metric or explicit target).
- Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
- Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
- If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.
- Save the spec file AFTER each integration to minimize risk of context loss (atomic overwrite).
- Preserve formatting: do not reorder unrelated sections; keep heading hierarchy intact.
- Keep each inserted clarification minimal and testable (avoid narrative drift).
7. Validation (performed after EACH write plus final pass):
- Clarifications session contains exactly one bullet per accepted answer (no duplicates).
- Total asked (accepted) questions ≤ 5.
- Updated sections contain no lingering vague placeholders the new answer was meant to resolve.
- No contradictory earlier statement remains (scan for now-invalid alternative choices removed).
- Markdown structure valid; only allowed new headings: `## Clarifications`, `### Session YYYY-MM-DD`.
- Terminology consistency: same canonical term used across all updated sections.
8. Write the updated spec back to `FEATURE_SPEC`.
9. **Re-validate Spec Quality Checklist** (if it exists):
- Check if `FEATURE_DIR/checklists/requirements.md` exists.
- If it does NOT exist, skip this step silently.
- If it exists:
1. Read the checklist file.
2. Identify all GitHub task-list checkbox lines — lines matching `- [ ]`, `- [x]`, or `- [X]` (case-insensitive, tolerant of leading whitespace for nested items) outside of code fences. Ignore all other content (headings, notes, non-checkbox bullets, metadata).
3. For each checkbox line, record its current marker state (checked or unchecked) and item text into a before-snapshot list.
4. Re-evaluate each checkbox item against the **updated** spec (the version just saved in step 7).
5. For each checkbox item, update only if the checked/unchecked state actually changes:
- If the item now passes and was unchecked: change `[ ]` to `[x]`.
- If the item now fails and was checked: change `[x]`/`[X]` to `[ ]`.
- If the state is unchanged: leave the marker as-is (preserve existing case to avoid cosmetic diffs).
6. Save the updated checklist file. **Only toggle the `[ ]`/`[x]` marker portion of checkbox lines whose state changed.** All other file content — headings, metadata, notes, line ordering, whitespace — must remain unchanged to avoid noisy diffs.
7. Compare the before-snapshot with the current state to compute three lists for the Completion Report:
- **Newly passing**: items that changed from unchecked to checked.
- **Regressions**: items that changed from checked to unchecked.
- **Still unchecked**: items that remain unchecked.
8. Record the before/after pass counts as checked/total checkbox items (e.g., "12/16 → 15/16 items passing").
Behavior rules:
- If no meaningful ambiguities found (or all potential questions would be low-impact), respond: "No critical ambiguities detected worth formal clarification." and suggest proceeding.
- If spec file missing, instruct user to run `__SPECKIT_COMMAND_SPECIFY__` first (do not create a new spec here).
- Never exceed 5 total asked questions (clarification retries for a single question do not count as new questions).
- Avoid speculative tech stack questions unless the absence blocks functional clarity.
- Respect user early termination signals ("stop", "done", "proceed").
- If no questions asked due to full coverage, output a compact coverage summary (all categories Clear) then suggest advancing.
- If quota reached with unresolved high-impact categories remaining, explicitly flag them under Deferred with rationale.
Context for prioritization: {ARGS}
## Mandatory Post-Execution Hooks
**You MUST complete this section before reporting completion to the user.**
Check if `.specify/extensions.yml` exists in the project root.
- If it does not exist, or no hooks are registered under `hooks.after_clarify`, skip to the Completion Report.
- If it exists, read it and look for entries under the `hooks.after_clarify` key.
- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
- If the hook has no `condition` field, or it is null/empty, treat the hook as executable
- If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
- For each executable hook, output the following based on its `optional` flag:
- **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
```
## Extension Hooks
**Automatic Hook**: {extension}
Executing: `/{command}`
EXECUTE_COMMAND: {command}
```
- **Optional hook** (`optional: true`):
```
## Extension Hooks
**Optional Hook**: {extension}
Command: `/{command}`
Description: {description}
Prompt: {prompt}
To execute: `/{command}`
```
## Completion Report
Report completion (after questioning loop ends or early termination):
- Number of questions asked & answered.
- Path to updated spec.
- Sections touched (list names).
- Spec quality checklist status (if `FEATURE_DIR/checklists/requirements.md` was re-validated): show before/after pass counts (e.g., "Spec Quality Checklist: 12/16 → 15/16 items passing") and list any items that changed state — both newly checked (unchecked → checked) and any regressions (checked → unchecked). If any items remain unchecked, list them as areas needing attention.
- Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
- If any Outstanding or Deferred remain, recommend whether to proceed to `__SPECKIT_COMMAND_PLAN__` or run `__SPECKIT_COMMAND_CLARIFY__` again later post-plan.
- Suggested next command.
## Done When
- [ ] Spec ambiguities identified and clarifications integrated into spec file
- [ ] Spec quality checklist re-validated against updated spec (if `FEATURE_DIR/checklists/requirements.md` exists)
- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
- [ ] Completion reported to user with questions answered, sections touched, checklist status, and coverage summary