chore: bump version to 0.12.7

On refresh (bundle update), install_bundle iterated only the new plan's
components, so a component the previous version owned but the new one no
longer ships was left installed on disk while being dropped from the
rewritten record (contributed only holds plan.components). With no
record referencing it, remove_bundle could never clean it up —
permanently orphaned, violating the provenance invariant (FR-022). After
the component loop, when refresh and a prior record exists, uninstall
each previously-owned component absent from the new plan — unless another
bundle still needs it (components_still_needed refcount, mirroring
remove_bundle), in which case it stays installed and is simply
de-attributed. Runs inside the existing try so a failed removal takes the
same no-record-written rollback path.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

CHANGELOG.md

@@ -2,6 +2,21 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.12.7] - 2026-07-07
+
+### Changed
+
+- fix(bundler): bundle update uninstalls components dropped by new version (#3353)
+- fix(workflows): route run/resume errors to stderr under --json (#3352)
+- fix(workflows): fan-in validate() rejects non-mapping output (#3349)
+- fix(workflows): shell step validate() rejects non-string run (#3348)
+- fix(integrations): agy honors SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (#3347)
+- Add Orchestration Task Context Management extension to community catalog (#3372)
+- Update DocGuard — CDD Enforcement extension to v0.30.0 (#3371)
+- Update Ripple extension to v1.1.0 (#3370)
+- feat(integrations): generalize post-processing to all format types (#3311)
+- chore: release 0.12.6, begin 0.12.7.dev0 development (#3393)
+
 ## [0.12.6] - 2026-07-07
 
 ### Changed

docs/community/extensions.md

@@ -51,7 +51,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
 | Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
 | Fix Findings | Automated analyze-fix-reanalyze loop that resolves spec findings until clean | `code` | Read+Write | [spec-kit-fix-findings](https://github.com/Quratulain-bilal/spec-kit-fix-findings) |
 | FixIt Extension | Spec-aware bug fixing — maps bugs to spec artifacts, proposes a plan, applies minimal changes | `code` | Read+Write | [spec-kit-fixit](https://github.com/speckit-community/spec-kit-fixit) |
@@ -86,6 +86,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |
+| Orchestration Task Context Management | Adds subagent work-unit orchestration to generated Spec Kit task files | `process` | Read+Write | [spec-kit-orchestration-task-context-management](https://github.com/benizzio/spec-kit-orchestration-task-context-management) |
 | OWASP LLM Threat Model | OWASP Top 10 for LLM Applications 2025 threat analysis on agent artifacts | `code` | Read-only | [spec-kit-threatmodel](https://github.com/NaviaSamal/spec-kit-threatmodel) |
 | Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
@@ -106,7 +107,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Retro Extension | Sprint retrospective analysis with metrics, spec accuracy assessment, and improvement suggestions | `process` | Read+Write | [spec-kit-retro](https://github.com/arunt14/spec-kit-retro) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| Ripple | Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
+| Ripple | Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Security Review | Full-project secure-by-design security audits plus staged, branch/PR, plan, task, follow-up, and apply reviews | `code` | Read+Write | [spec-kit-security-review](https://github.com/DyanGalih/spec-kit-security-review) |
 | SFSpeckit | Enterprise Salesforce SDLC with 18 commands for the full SDD lifecycle. | `process` | Read+Write | [spec-kit-sf](https://github.com/ysumanth06/spec-kit-sf) |

extensions/catalog.community.json

@@ -1106,10 +1106,10 @@
     "docguard": {
       "name": "DocGuard — CDD Enforcement",
       "id": "docguard",
-      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise.",
+      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
       "author": "raccioly",
-      "version": "0.28.0",
+      "version": "0.30.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.zip",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
       "repository": "https://github.com/raccioly/docguard",
       "homepage": "https://www.npmjs.com/package/docguard-cli",
       "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -1145,7 +1145,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
     },
     "doctor": {
       "name": "Project Health Check",
@@ -2396,6 +2396,39 @@
       "created_at": "2026-04-03T00:00:00Z",
       "updated_at": "2026-04-03T00:00:00Z"
     },
+    "orchestration-task-context-management": {
+      "name": "Orchestration Task Context Management",
+      "id": "orchestration-task-context-management",
+      "description": "Adds subagent work-unit orchestration to generated Spec Kit task files",
+      "author": "Igor Benicio de Mesquita",
+      "version": "0.0.0",
+      "download_url": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/archive/refs/tags/v0.0.0.zip",
+      "repository": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "homepage": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "documentation": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/README.md",
+      "changelog": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.7.2"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 2
+      },
+      "tags": [
+        "agent",
+        "orchestration",
+        "tasks",
+        "context"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
     "orchestrator": {
       "name": "Spec Orchestrator",
       "id": "orchestrator",
@@ -3086,10 +3119,10 @@
     "ripple": {
       "name": "Ripple",
       "id": "ripple",
-      "description": "Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories with fix-induced side effect detection",
+      "description": "Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories",
       "author": "chordpli",
-      "version": "1.0.0",
+      "version": "1.1.0",
-      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.zip",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.1.0.zip",
       "repository": "https://github.com/chordpli/spec-kit-ripple",
       "homepage": "https://github.com/chordpli/spec-kit-ripple",
       "documentation": "https://github.com/chordpli/spec-kit-ripple/blob/main/README.md",
@@ -3098,7 +3131,13 @@
       "category": "code",
       "effect": "read-write",
       "requires": {
-        "speckit_version": ">=0.2.0"
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          {
+            "name": "git",
+            "required": true
+          }
+        ]
       },
       "provides": {
         "commands": 3,
@@ -3115,7 +3154,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-04-20T00:00:00Z",
-      "updated_at": "2026-04-20T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
     },
     "roadmap": {
       "name": "Spec Roadmap",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.6"
+version = "0.12.7"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 readme = "README.md"
 requires-python = ">=3.11"

src/specify_cli/agents.py

@@ -706,6 +706,17 @@ class CommandRegistrar:
             else:
                 raise ValueError(f"Unsupported format: {agent_config['format']}")
 
+            # -- Post-process for non-skills agents -----------------------
+            _integration = None
+            if agent_config["extension"] != "/SKILL.md":
+                from specify_cli.integrations import (  # noqa: PLC0415
+                    get_integration,
+                )
+
+                _integration = get_integration(agent_name)
+                if _integration is not None:
+                    output = _integration.post_process_command_content(output)
+
             dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
             self._ensure_inside(dest_file, commands_dir)
             dest_file.parent.mkdir(parents=True, exist_ok=True)
@@ -766,6 +777,9 @@ class CommandRegistrar:
                         raise ValueError(
                             f"Unsupported format: {agent_config['format']}"
                         )
+
+                    if agent_config["extension"] != "/SKILL.md" and _integration is not None:
+                        alias_output = _integration.post_process_command_content(alias_output)
                 else:
                     # For other agents, reuse the primary output
                     alias_output = output

src/specify_cli/bundler/services/installer.py

@@ -130,6 +130,28 @@ def install_bundle(
             done.append(component)
             result.installed.append(component)
             contributed.append(component)
+
+        # On update (refresh), uninstall components this bundle used to own
+        # that the new version no longer ships. Otherwise they are dropped
+        # from the record below (contributed only holds plan.components) yet
+        # left on disk — permanently orphaned, since no bundle record can
+        # ever remove them. A stale component still owned by another bundle
+        # is kept installed and simply de-attributed here (it stays in that
+        # bundle's record). Mirrors remove_bundle's refcount logic.
+        if refresh and existing is not None:
+            planned = {(c.kind, c.id) for c in plan.components}
+            still_needed = components_still_needed(
+                records, exclude_bundle_id=plan.bundle_id
+            )
+            for component in existing.contributed_components:
+                key = (component.kind, component.id)
+                if key in planned:
+                    continue
+                if key in still_needed:
+                    continue
+                if installer.is_installed(project_root, component):
+                    installer.remove(project_root, component)
+                    result.uninstalled.append(component)
     except BundlerError:
         _rollback(project_root, installer, done)
         raise

src/specify_cli/integrations/agy/__init__.py

@@ -89,7 +89,11 @@ class AgyIntegration(SkillsIntegration):
         output_json: bool = True,
     ) -> list[str] | None:
         # agy does not support --model or JSON output; both params are ignored
-        return [self._resolve_executable(), "--print", prompt]
+        args = [self._resolve_executable(), "--print", prompt]
+        # Honor SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (operator-supplied flags),
+        # appended after the positional prompt like the devin integration.
+        self._apply_extra_args_env_var(args)
+        return args
 
     def setup(
         self,

src/specify_cli/integrations/base.py

@@ -123,6 +123,19 @@ class IntegrationBase(ABC):
     integration that sets this flag.
     """
 
+    def post_process_command_content(self, content: str) -> str:
+        """Transform command content after format rendering.
+
+        Called by ``register_commands()`` for non-skills format types
+        (Markdown, TOML, YAML) after the command has been rendered into
+        its target format and before writing to disk.  Skills-format
+        agents use ``post_process_skill_content()`` instead.
+
+        Subclasses may override to inject agent-specific content.
+        The default implementation returns *content* unchanged.
+        """
+        return content
+
     # -- Public API -------------------------------------------------------
 
     @classmethod

src/specify_cli/workflows/_commands.py

@@ -50,7 +50,17 @@ workflow_step_catalog_app = typer.Typer(
 workflow_step_app.add_typer(workflow_step_catalog_app, name="catalog")
 
 
-def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
+def _error_console(json_output: bool):
+    """Console for error text: stderr under ``--json`` so the JSON stdout
+    stream stays parseable, the normal console otherwise. Mirrors the
+    stderr-only error routing already used by ``specify bundle``.
+    """
+    return err_console if json_output else console
+
+
+def _parse_input_values(
+    input_values: list[str] | None, *, json_output: bool = False
+) -> dict[str, Any]:
     """Parse repeated ``key=value`` CLI inputs into a dict.
 
     Shared by ``workflow run`` and ``workflow resume``. Exits with an error
@@ -59,7 +69,9 @@ def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
     inputs: dict[str, Any] = {}
     for kv in input_values or []:
         if "=" not in kv:
-            console.print(f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)")
+            _error_console(json_output).print(
+                f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)"
+            )
             raise typer.Exit(1)
         key, _, value = kv.partition("=")
         inputs[key.strip()] = value.strip()
@@ -335,25 +347,26 @@ def workflow_run(
     if not json_output:
         engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")
 
+    err = _error_console(json_output)
     try:
         definition = engine.load_workflow(source_path if is_file_source else source)
     except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Workflow not found: {source}")
+        err.print(f"[red]Error:[/red] Workflow not found: {source}")
         raise typer.Exit(1)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] Invalid workflow: {exc}")
+        err.print(f"[red]Error:[/red] Invalid workflow: {exc}")
         raise typer.Exit(1)
 
     # Validate
     errors = engine.validate(definition)
     if errors:
-        console.print("[red]Workflow validation failed:[/red]")
+        err.print("[red]Workflow validation failed:[/red]")
-        for err in errors:
+        for verr in errors:
-            console.print(f"  • {err}")
+            err.print(f"  • {verr}")
         raise typer.Exit(1)
 
     # Parse inputs
-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)
 
     if not json_output:
         console.print(f"\n[bold cyan]Running workflow:[/bold cyan] {definition.name} ({definition.id})")
@@ -363,10 +376,10 @@ def workflow_run(
         with _stdout_to_stderr_when(json_output):
             state = engine.execute(definition, inputs)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
         raise typer.Exit(1)
     except Exception as exc:
-        console.print(f"[red]Workflow failed:[/red] {exc}")
+        err.print(f"[red]Workflow failed:[/red] {exc}")
         raise typer.Exit(1)
 
     if json_output:
@@ -411,19 +424,20 @@ def workflow_resume(
     if not json_output:
         engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")
 
-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)
+    err = _error_console(json_output)
 
     try:
         with _stdout_to_stderr_when(json_output):
             state = engine.resume(run_id, inputs or None)
     except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Run not found: {run_id}")
+        err.print(f"[red]Error:[/red] Run not found: {run_id}")
         raise typer.Exit(1)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
         raise typer.Exit(1)
     except Exception as exc:
-        console.print(f"[red]Resume failed:[/red] {exc}")
+        err.print(f"[red]Resume failed:[/red] {exc}")
         raise typer.Exit(1)
 
     if json_output:

src/specify_cli/workflows/steps/fan_in/__init__.py

@@ -58,4 +58,13 @@ class FanInStep(StepBase):
                 f"Fan-in step {config.get('id', '?')!r}: "
                 f"'wait_for' must be a non-empty list of step IDs."
             )
+        output = config.get("output")
+        if output is not None and not isinstance(output, dict):
+            # execute() silently coerces a non-mapping output to {}, so the
+            # author's declared aggregation keys would vanish with no error.
+            # Reject at validation, mirroring the command-step (#3262) fix.
+            errors.append(
+                f"Fan-in step {config.get('id', '?')!r}: 'output' must be a "
+                f"mapping of key -> expression, got {type(output).__name__}."
+            )
         return errors

src/specify_cli/workflows/steps/shell/__init__.py

@@ -90,6 +90,16 @@ class ShellStep(StepBase):
             errors.append(
                 f"Shell step {config.get('id', '?')!r} is missing 'run' field."
             )
+        elif not isinstance(config["run"], str):
+            # execute() str()-coerces run and invokes it under shell=True, so a
+            # null or list 'run' would run the Python repr ('None', "['echo']")
+            # as a command. Reject non-strings at validation, mirroring the
+            # command-step input/options and gate options type checks. An
+            # expression like "{{ ... }}" is still a str, so it stays valid.
+            errors.append(
+                f"Shell step {config.get('id', '?')!r}: 'run' must be a string, "
+                f"got {type(config['run']).__name__}."
+            )
         output_format = config.get("output_format")
         if output_format is not None and output_format != "json":
             errors.append(

tests/integration/test_bundler_install_flow.py

@@ -220,3 +220,68 @@ def test_pre_existing_component_is_not_attributed_or_removed(tmp_path: Path):
 
     remove_bundle(tmp_path, "demo-bundle", installer)
     assert ("extensions", "ext-a") in installer.installed
+
+
+def _bundle(manifest_id, ext_ids, *, version="1.0.0"):
+    data = valid_manifest_dict()
+    data["bundle"]["id"] = manifest_id
+    data["bundle"]["version"] = version
+    data["provides"] = {
+        "extensions": [{"id": e, "version": version} for e in ext_ids]
+    }
+    return BundleManifest.from_dict(data)
+
+
+def test_update_uninstalls_components_dropped_by_new_version(tmp_path: Path):
+    """`bundle update` must uninstall components the new version no longer
+    ships, instead of orphaning them (installed on disk, tracked by nothing)."""
+    make_project(tmp_path)
+    installer = FakeInstaller()
+
+    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
+    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
+    assert ("extensions", "ext-b") in installer.installed
+
+    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
+    result = install_bundle(
+        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
+    )
+
+    # ext-b was dropped by v2 -> uninstalled and reported.
+    assert ("extensions", "ext-b") in installer.remove_calls
+    assert ("extensions", "ext-b") in {(c.kind, c.id) for c in result.uninstalled}
+    assert ("extensions", "ext-b") not in installer.installed
+    assert ("extensions", "ext-a") in installer.installed
+
+    # The saved record lists only ext-a.
+    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
+    keys = {(c.kind, c.id) for c in rec.contributed_components}
+    assert ("extensions", "ext-a") in keys
+    assert ("extensions", "ext-b") not in keys
+
+
+def test_update_keeps_component_still_needed_by_sibling_bundle(tmp_path: Path):
+    """A dropped component still owned by another bundle stays installed."""
+    make_project(tmp_path)
+    installer = FakeInstaller()
+
+    man_sib = _bundle("sibling", ["ext-b"])
+    install_bundle(tmp_path, _plan(man_sib), installer, manifest=man_sib)
+
+    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
+    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
+
+    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
+    install_bundle(
+        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
+    )
+
+    # ext-b is still needed by 'sibling' -> not removed, stays installed.
+    assert ("extensions", "ext-b") not in installer.remove_calls
+    assert ("extensions", "ext-b") in installer.installed
+
+    # But demo's record no longer attributes it.
+    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
+    assert ("extensions", "ext-b") not in {
+        (c.kind, c.id) for c in rec.contributed_components
+    }

tests/integrations/test_integration_agy.py

@@ -81,6 +81,26 @@ class TestAgyBuildExecArgs:
         result = i.build_exec_args("my prompt", output_json=False)
         assert result == ["agy", "--print", "my prompt"]
 
+    def test_build_exec_args_honors_extra_args(self, monkeypatch):
+        """SPECKIT_INTEGRATION_AGY_EXTRA_ARGS must be appended after the prompt.
+
+        agy previously skipped _apply_extra_args_env_var entirely, so the
+        documented per-integration extra-args hook was silently ignored
+        (same class as the merged cursor-agent fix #3265).
+        """
+        from specify_cli.integrations import get_integration
+        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXTRA_ARGS", "--verbose")
+        i = get_integration("agy")
+        assert i.build_exec_args("my prompt") == [
+            "agy", "--print", "my prompt", "--verbose",
+        ]
+
+    def test_build_exec_args_honors_executable_override(self, monkeypatch):
+        from specify_cli.integrations import get_integration
+        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXECUTABLE", "/custom/agy")
+        i = get_integration("agy")
+        assert i.build_exec_args("my prompt")[0] == "/custom/agy"
+
 
 class TestAgyHookCommandNote:
     """Verify dot-to-hyphen normalization note is injected into hook sections."""

tests/test_post_process.py

@@ -0,0 +1,245 @@
+"""Tests for post_process_command_content() hook on IntegrationBase.
+
+Verifies that the generalized post-processing hook:
+- Runs for non-skills format types (Markdown, TOML, YAML)
+- Does NOT run for skills-format agents
+- Default no-op returns content unchanged
+- Exceptions propagate to caller
+"""
+
+from __future__ import annotations
+
+from unittest.mock import patch
+
+import pytest
+
+from specify_cli.agents import CommandRegistrar
+from specify_cli.integrations.base import IntegrationBase
+
+
+@pytest.fixture
+def registrar():
+    return CommandRegistrar()
+
+
+@pytest.fixture
+def ext_dir(tmp_path):
+    """Create a mock extension with a simple command template."""
+    ext = tmp_path / "extension"
+    ext.mkdir()
+    cmd_dir = ext / "commands"
+    cmd_dir.mkdir()
+    return ext, cmd_dir
+
+
+def _write_cmd(cmd_dir, name="review.md", body="Review the code.\n"):
+    cmd_file = cmd_dir / name
+    cmd_file.write_text(
+        f"---\ndescription: Test command\n---\n\n{body}",
+        encoding="utf-8",
+    )
+    return cmd_file
+
+
+class TestDefaultNoOp:
+    def test_returns_content_unchanged(self):
+        base = IntegrationBase()
+        content = "Some command content\nwith multiple lines."
+        assert base.post_process_command_content(content) == content
+
+    def test_empty_string(self):
+        base = IntegrationBase()
+        assert base.post_process_command_content("") == ""
+
+
+class TestMarkdownAgentPostProcess:
+    def test_opencode_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        opencode = get_integration("opencode")
+        marker = "<!-- POST_PROCESSED -->"
+
+        def _inject_marker(self, content):
+            return content + marker
+
+        monkeypatch.setattr(
+            opencode.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "opencode", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".opencode" / "commands" / "speckit.test.review.md"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestTomlAgentPostProcess:
+    def test_gemini_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        gemini = get_integration("gemini")
+        marker = "# POST_PROCESSED"
+
+        def _inject_marker(self, content):
+            return content + f"\n{marker}\n"
+
+        monkeypatch.setattr(
+            gemini.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "gemini", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".gemini" / "commands" / "speckit.test.review.toml"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestYamlAgentPostProcess:
+    def test_goose_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        goose = get_integration("goose")
+        marker = "# POST_PROCESSED"
+
+        def _inject_marker(self, content):
+            return content + f"\n{marker}\n"
+
+        monkeypatch.setattr(
+            goose.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "goose", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".goose" / "recipes" / "speckit.test.review.yaml"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestSkillsAgentExcluded:
+    def test_claude_post_process_not_called(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        claude = get_integration("claude")
+        marker = "<!-- SHOULD_NOT_APPEAR -->"
+
+        def _inject_marker(self, content):
+            return content + marker
+
+        monkeypatch.setattr(
+            claude.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "claude", commands, "test-ext", ext, tmp_path
+        )
+
+        skill_file = (
+            tmp_path / ".claude" / "skills" / "speckit-test-review" / "SKILL.md"
+        )
+        assert skill_file.exists()
+        content = skill_file.read_text(encoding="utf-8")
+        assert marker not in content
+
+    def test_skills_agent_method_never_called(
+        self, tmp_path, registrar, ext_dir
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        claude = get_integration("claude")
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+
+        with patch.object(
+            claude.__class__, "post_process_command_content", wraps=claude.post_process_command_content
+        ) as mock_method:
+            registrar.register_commands(
+                "claude", commands, "test-ext", ext, tmp_path
+            )
+            mock_method.assert_not_called()
+
+
+class TestExceptionPropagation:
+    def test_hook_exception_propagates(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        opencode = get_integration("opencode")
+
+        def _raise(self, content):
+            raise RuntimeError("Hook failed")
+
+        monkeypatch.setattr(
+            opencode.__class__, "post_process_command_content", _raise
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        with pytest.raises(RuntimeError, match="Hook failed"):
+            registrar.register_commands(
+                "opencode", commands, "test-ext", ext, tmp_path
+            )
+
+
+class TestRegressionPlainTemplate:
+    @pytest.mark.parametrize(
+        "agent,path_pattern",
+        [
+            ("claude", ".claude/skills/speckit-test-plain/SKILL.md"),
+            ("opencode", ".opencode/commands/speckit.test.plain.md"),
+        ],
+        ids=["skills", "markdown"],
+    )
+    def test_plain_template_unchanged(
+        self, tmp_path, registrar, ext_dir, agent, path_pattern
+    ):
+        ext, cmd_dir = ext_dir
+        body_text = "This is a plain command with no special content.\n"
+        _write_cmd(cmd_dir, name="plain.md", body=body_text)
+
+        commands = [{"name": "speckit.test.plain", "file": "commands/plain.md"}]
+        registrar.register_commands(
+            agent, commands, "test-ext", ext, tmp_path
+        )
+
+        output_file = tmp_path / path_pattern
+        assert output_file.exists(), f"Output file missing for {agent}"
+        content = output_file.read_text(encoding="utf-8")
+        assert body_text.strip() in content, f"Body text missing in {agent} output"

tests/test_workflow_run_without_project.py

@@ -322,3 +322,87 @@ class TestWorkflowRunWithoutProject:
 
         assert result.exit_code != 0
         assert ".specify path exists but is not a directory" in result.output
+
+
+class TestWorkflowRunJsonErrorStream:
+    """Under --json, error text must go to stderr so stdout stays parseable."""
+
+    def _bad_workflow(self, tmp_path):
+        wf = tmp_path / "bad.yml"
+        wf.write_text(
+            yaml.dump(
+                {
+                    "schema_version": "1.0",
+                    "workflow": {
+                        "id": "bad-wf",
+                        "name": "Bad",
+                        "version": "1.0.0",
+                        "description": "fails validation",
+                    },
+                    # shell step missing required 'run' -> validation error
+                    "steps": [{"id": "s", "type": "shell"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+        return wf
+
+    def test_run_json_validation_error_not_on_stdout(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        wf = self._bad_workflow(tmp_path)
+        runner = CliRunner()
+        old = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(
+                app, ["workflow", "run", str(wf), "--json"], catch_exceptions=False
+            )
+        finally:
+            os.chdir(old)
+
+        assert result.exit_code == 1
+        # stdout must carry only JSON (here: nothing) — never human error text.
+        assert "validation failed" not in result.stdout
+        assert "Error" not in result.stdout
+        # The message is routed to stderr instead.
+        assert "validation failed" in result.stderr
+
+    def test_run_json_invalid_input_not_on_stdout(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        # A valid single-shell workflow so we get past load/validate to
+        # _parse_input_values, which rejects the malformed --input.
+        wf = tmp_path / "ok.yml"
+        wf.write_text(
+            yaml.dump(
+                {
+                    "schema_version": "1.0",
+                    "workflow": {
+                        "id": "ok-wf",
+                        "name": "OK",
+                        "version": "1.0.0",
+                        "description": "x",
+                    },
+                    "steps": [{"id": "s", "type": "shell", "run": "echo hi"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+        runner = CliRunner()
+        old = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(
+                app,
+                ["workflow", "run", str(wf), "--json", "--input", "no-equals"],
+                catch_exceptions=False,
+            )
+        finally:
+            os.chdir(old)
+
+        assert result.exit_code == 1
+        assert "Invalid input format" not in result.stdout
+        assert "Invalid input format" in result.stderr

tests/test_workflows.py

@@ -1266,6 +1266,26 @@ class TestShellStep:
         errors = step.validate({"id": "test"})
         assert any("missing 'run'" in e for e in errors)
 
+    @pytest.mark.parametrize("bad_run", [None, ["echo", "hi"], 42])
+    def test_validate_rejects_non_string_run(self, bad_run):
+        """A non-string 'run' must be rejected at validation.
+
+        execute() str()-coerces run and invokes it under shell=True, so a
+        null or list run would otherwise run the Python repr as a command.
+        """
+        from specify_cli.workflows.steps.shell import ShellStep
+
+        step = ShellStep()
+        errors = step.validate({"id": "s", "run": bad_run})
+        assert any("'run' must be a string" in e for e in errors)
+
+    def test_validate_accepts_string_and_expression_run(self):
+        from specify_cli.workflows.steps.shell import ShellStep
+
+        step = ShellStep()
+        assert step.validate({"id": "s", "run": "echo hi"}) == []
+        assert step.validate({"id": "s", "run": "{{ steps.x.output }}"}) == []
+
 
     def test_output_format_json_exposes_data(self, tmp_path):
         from specify_cli.workflows.steps.shell import ShellStep
@@ -2182,6 +2202,27 @@ class TestFanInStep:
         errors = step.validate({"id": "test", "wait_for": "not-a-list"})
         assert any("non-empty list" in e for e in errors)
 
+    @pytest.mark.parametrize("bad_output", [["{{ fan_in.results }}"], "{{ x }}", 42])
+    def test_validate_rejects_non_mapping_output(self, bad_output):
+        """A non-mapping 'output' must be rejected: execute() would otherwise
+        silently coerce it to {} and drop the declared aggregation keys."""
+        from specify_cli.workflows.steps.fan_in import FanInStep
+
+        step = FanInStep()
+        errors = step.validate(
+            {"id": "j", "wait_for": ["a"], "output": bad_output}
+        )
+        assert any("'output' must be a mapping" in e for e in errors)
+
+    def test_validate_accepts_mapping_or_absent_output(self):
+        from specify_cli.workflows.steps.fan_in import FanInStep
+
+        step = FanInStep()
+        assert step.validate(
+            {"id": "j", "wait_for": ["a"], "output": {"joined": "{{ x }}"}}
+        ) == []
+        assert step.validate({"id": "j", "wait_for": ["a"]}) == []
+
 
 class TestFanOutConcurrency:
     """Fan-out honors max_concurrency (WorkflowEngine._run_fan_out)."""