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github-actions[bot]
fdfc5ae330 Add ContextForge MCP extension to community catalog (#3487) 
Add contextforge-mcp extension submitted by @capatinore to:
- extensions/catalog.community.json (alphabetical order)
- docs/community/extensions.md community extensions table

Closes #3456

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-30 07:49:40 -05:00
Markus Wondrak
675143591d feat: bind gate verdict to workflow input via verdict_input (#3725) 
* feat: bind gate verdict to workflow input via verdict_input

Add an optional `verdict_input` field to gate steps that lets an
external system supply a verdict through a declared workflow input
instead of an interactive TTY prompt.

When the referenced input carries a non-empty string value that
matches one of the gate's `options` (case-insensitive), the gate
auto-decides, records the matched spelling in `output.choice`, and
applies the existing `on_reject` / abort / skip / retry semantics.
If the value is present but does not match an option, or is a
non-string, the gate fails immediately with a clear error message.
When the input is absent, null, or empty, the gate falls back to
today's TTY-prompt-or-pause behaviour unchanged.

The engine now persists `result.error` alongside each step's status
and output so that failed-step error messages survive across runs.
The CLI (`workflow run` and `workflow resume`) surfaces these
persisted errors after a failed or aborted run. `validate_workflow`
cross-references `verdict_input` against the workflow's declared
inputs block and reports an error for undeclared names, consistent
with the existing `wait_for` id cross-check.

Closes discussion: https://github.com/github/spec-kit/discussions/3717

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Fix workflow JSON error payloads

Include persisted step errors in _workflow_run_payload so workflow run/resume/status --json all surface failure reasons consistently. Add JSON-path tests for failed and successful runs.

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(workflows): reject verdict inputs in fan-out

Fan-out items share workflow inputs and cannot safely consume a bound gate verdict. Reject verdict_input bindings during validation and at runtime while preserving unbound gates.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: update workflow command handling

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Markus <markus@example.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
 2026-07-30 07:39:49 -05:00
github-actions[bot]
5827db5359 Add Intent Reconciliation extension to community catalog (#3858) 
Add `intent` extension submitted by @SuhaibAslam to:
- extensions/catalog.community.json (inserted alphabetically between intake and issue)
- docs/community/extensions.md community extensions table

This revision limits the catalog change to the intent addition and the
top-level updated_at bump only, reverting the unrelated re-serialization
(entry reordering, \u2014 Unicode escaping, tool-array reformatting) that a
reviewer flagged.

Closes #3854
cc @SuhaibAslam

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
 2026-07-29 12:58:32 -05:00
github-actions[bot]
4ad7ef2b42 Update Agent Parity Governance preset to v0.4.1 (#3830) 
Update agent-parity-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, updated_at)
- docs/community/presets.md community presets table

Closes #3829

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-28 17:25:54 -05:00
github-actions[bot]
0231ee056b [preset] Update A11Y Governance preset to v0.4.2 (#3828) 
* Update A11Y Governance preset to v0.4.2

Update a11y-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, updated_at)
- docs/community/presets.md community presets table

Closes #3827

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
 2026-07-28 16:55:37 -05:00
github-actions[bot]
ca2b494335 [preset] Update Parallel Autonomous Run Governance to v0.2.4 (#3825) 
* Update Parallel Autonomous Run Governance preset to v0.2.4

Update parallel-autonomous-run-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, documentation, description, requires.extensions, tags, updated_at)
- docs/community/presets.md community presets table

Closes #3824

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
 2026-07-28 16:23:34 -05:00
github-actions[bot]
9bb7206d3b Update Autonomous Run Governance preset to v0.3.3 (#3823) 
Update autonomous-run-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, tags, updated_at)
- docs/community/presets.md community presets table

Closes #3821

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-28 15:18:57 -05:00
github-actions[bot]
186ca25c99 Update Intake Sequencing Governance preset to v0.2.2 (#3809) 
Update intake-sequencing-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, provides)
- docs/community/presets.md community presets table

Closes #3807

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-28 13:18:10 -05:00
github-actions[bot]
809b4c5e26 Update Intake Review Governance preset to v0.2.0 (#3796) 
Update intake-review-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, documentation, description, scripts, tags)
- docs/community/presets.md community presets table

Closes #3794

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-28 09:37:09 -05:00
github-actions[bot]
d8d62756fe Update Intake Authoring Governance preset to v0.3.0 (#3788) 
Update intake-authoring-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, provides, tags, updated_at)
- docs/community/presets.md community presets table

Closes #3780

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-28 08:34:17 -05:00
Eric X Engstfeld
7fc5b236c8 feat: Add Alquimia AI integration (#2734) 
* Add alquimia-ai as new integration: https://alquimia.ai

* Fix test cases for alquimia-ai integration. Add alquimia-ai to workflow.yml

* Add install url to alquimia-ai integration

* Renamed alquimia-ai to alquimia (cli native denomination)

* Fix unit tests for alquimia integration

* Minor fix in alquimia integration

* Fix typos and copilot findings

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Update tests cases and lint formatting

* Final fixes

* Rename alquimia_ai to alquimia module integration

* Make cli optional for alquimiia integration

* resolve review comments

* Fix copilot review

* Minor fixes: naming, remove unused code

* Update tests cases. Fix issues

* Fix unit tests

* Add alquimia context to default agent-context extension. Update cli requirment to support workflows

* Fix hints (suggestion)

* Add Alquimia AI as agent in github issue template. Fix unit tests

* Address review comments. Update docs

* Update test cases

---------

Co-authored-by: Eric Engstfeld <ericengstfeld@Erics-MacBook-Pro.local>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
 2026-07-28 07:54:13 -05:00
Marsel Safin
683bfd00c9 fix: register extensions for the active integration only (#3459) 
* fix: register extensions for the active integration only

extension add registered commands for every detected agent, and
integration upgrade back-filled enabled extensions for non-active
integrations. Maintainer direction on #2948: treat the project as
single-active. Only the active integration gets extension artifacts;
use/switch rescaffold the target when the user selects it.

- extension add now routes through the all-agents pass restricted to
  the active integration (only_agent), keeping detection and
  missing-skills-dir recovery safeguards. Projects without recorded
  init-options fall back to detection-based registration.
- integration upgrade re-registers extensions only when upgrading the
  active integration, reversing the #2886 back-fill for non-active
  targets at maintainer request.

Fixes #2948

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address review feedback on active-only extension registration

- Restrict the extension-add active-integration fallback to projects
  with no recorded active key at all. A recorded but unsupported key
  (e.g. "generic", deliberately excluded from AGENT_CONFIGS) no longer
  falls back to registering every detected agent.
- Apply the same single-active rule to preset command overrides:
  PresetManager._register_commands now scopes registration to the
  active integration via only_agent.
- Add PresetManager.register_enabled_presets_for_agent, mirroring
  ExtensionManager.register_enabled_extensions_for_agent, and call it
  from integration use/switch/upgrade (active only) alongside the
  existing extension re-registration so presets are rescaffolded on
  activation instead of being written for inactive integrations.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address second round of review feedback (priority order, fail-closed, docs)

- register_enabled_presets_for_agent now processes presets in reverse
  priority order (lowest-precedence first) so the highest-precedence
  preset is written last and actually wins after `integration use`
  rescaffolds two overlapping preset command overrides. Verified this
  reproduces the previously reported reversed-priority bug and that the
  fix resolves it.
- _register_commands_for_active_agent now checks for the "ai" key's
  presence separately from its value: a missing key still falls back to
  detection-based registration for all agents, but a recorded, malformed
  value (non-string or empty, e.g. [] or null) now fails closed
  (registers nothing) instead of being treated as "no active
  integration" or reaching AGENT_CONFIGS.get() with an unhashable key
  and raising TypeError.
- Updated docs/reference/presets.md and docs/reference/integrations.md
  to describe active-only preset/extension registration and clarify
  that `integration use`/`switch` is the activation point for
  installed extensions and presets, and that `upgrade` only
  re-registers them for the active integration.

Adds regression tests: two enabled presets overriding the same command
with different priorities (priority winner must survive `use`
rescaffolding), and a malformed recorded `ai` value ([]) for
`extension add`.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address third round of review feedback (multi-integration semantics)

Fixes five deeper active-only registration bugs surfaced by Copilot review
after 2486c08, all in the presets/extensions single-active integration
rule (#2948):

1. presets: _reconcile_composed_commands (run after install/remove)
   bypassed the active-only filter entirely, writing composition-winner
   command files for every detected non-skill agent via
   register_commands_for_non_skill_agents. Added an only_agent param to
   that registrar method (mirroring register_commands_for_all_agents)
   and threaded it through all 5 reconciliation call sites.

2. presets: `integration use copilot` with --skills (ai_skills: true)
   wrote both the static .agent.md command file AND the SKILL.md
   mirror for the same override. Mirrored the extension path's
   ai_skills guard in both _register_commands and the reconciliation
   pass: a command-backed active agent running in skills mode is
   excluded from non-skill command registration.

3. presets: registered_skills was a flat list, so switching between
   two skill-mode agents (e.g. Claude -> Codex) and then removing the
   preset only restored the currently active agent's directory,
   permanently orphaning the other. _unregister_skills now restores
   every existing skill-mode agent directory instead of only the
   active one.

4. extensions: load_init_options() collapses "no file" and "corrupted
   file" into the same {}, so the round-2 fail-closed fix didn't
   actually distinguish them. Added a shared
   resolve_active_agent_for_registration() helper in _init_options.py
   that checks file existence separately from parse success, returning
   a distinct sentinel for "file absent" vs None for "corrupted or
   invalid". extensions/__init__.py now uses this helper.

5. presets: same corruption-collapsing bug in _register_commands's
   active_agent resolution. Now uses the same shared helper as (4).

Adds regression tests for all five: reconciliation active-only
filtering, copilot --skills dual-write prevention, multi-skill-agent
switch+remove, and corrupted init-options fail-closed behavior for
both extension add and preset add. Each test was verified to fail
against the pre-fix code and pass with the fix.

Targeted (883) and full (3923 passed, 109 skipped) suites pass; ruff
check clean.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address fourth round of review feedback (skill registration provenance)

Replace the "enumerate every skill-mode directory and restore all of them"
approach from the previous round with precise per-agent provenance
tracking, per reviewer feedback that the enumerate-and-restore-everything
design was unsound:

- registered_skills changes from a flat List[str] to Dict[str, List[str]]
  (agent name -> skill names actually written), mirroring the shape
  registered_commands already uses. _register_skills now returns this
  per-agent mapping instead of a bare list, and every call site
  (register_enabled_presets_for_agent, install_from_directory, the
  _reconcile_skills "was this skill previously managed" check) is updated
  to read/merge the new shape. Legacy flat-list registry entries from
  before this change are still readable: writes self-migrate the format,
  and _normalize_registered_skills() handles the transitional read paths.

- _unregister_skills now restores exactly the agent directories recorded
  for a preset instead of guessing at every skill-mode integration that
  happens to exist on disk. This fixes two problems with the old
  enumerate-everything design: (1) it could silently overwrite or delete
  another preset's (or a user's) override in an agent directory the
  current preset never actually touched, and (2) it depended on
  transient per-process integration state (_skills_mode), which is unset
  in a fresh CLI invocation for mode-selectable integrations like Copilot
  --skills, permanently orphaning their overrides after a process
  restart. Registries written before this change (flat list, no agent
  provenance) fall back to best-effort restoration under only the
  currently active agent, matching the pre-existing guarantee level.

- Every directory resolved from persisted provenance is now validated
  through the project's shared symlink/containment guard
  (_ensure_safe_shared_directory) before any file in it is read, written,
  or removed, since restoration may target an agent that isn't currently
  active and its directory can't be assumed safe just because a name was
  recorded for it.

- _tracked_skill_agent_dirs() (the enumeration helper introduced last
  round) is removed; it's superseded by the provenance-based design.

Adds regression tests: a symlinked skills directory is rejected during
removal; removing one preset does not disturb a different preset's
override in another agent's directory; and a Copilot --skills
registration installed, then removed after switching agents in a fresh
PresetManager instance (simulating a new process), is still correctly
restored. Updates existing skill-registration assertions across
test_presets.py and test_integration_claude.py for the new per-agent
registry shape.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address fifth round of review feedback (symlink presence, rescaffold reconciliation, shared skills dir)

- _init_options.py: resolve_active_agent_for_registration() now treats a
  dangling init-options.json symlink as present (path.is_symlink() check
  alongside path.exists()), since Path.exists() follows symlinks and
  returns False for a broken one. Previously a broken symlink fell back
  to the legacy "no file" path and registered every detected agent
  instead of failing closed.
- presets/__init__.py (register_enabled_presets_for_agent): the
  integration use/switch rescaffold path now collects affected command
  names across all presets processed and runs
  _reconcile_composed_commands/_reconcile_skills once after the loop,
  matching install/remove. Previously rescaffolding wrote each preset's
  raw content directly with no follow-up reconciliation, so a
  project-level override (the highest-priority layer) could be clobbered
  by a lower-precedence preset after switching agents.
- presets/__init__.py (_unregister_skills): multiple integrations can
  share one physical skills directory (agy/codex/zed all resolve to
  .agents/skills). Provenance restoration now groups recorded agent
  entries by resolved directory and restores each physical directory
  exactly once, preferring the currently active agent's renderer when it
  owns that directory (otherwise any recorded owner, chosen
  deterministically). Previously each recorded agent key triggered its
  own restore pass against the same directory, with whichever agent was
  iterated last silently winning regardless of which agent was active.

Adds regression tests for each: a dangling init-options.json symlink
failing closed for both preset resolution and extension add; integration
use rescaffold preserving a project override over a lower-priority
preset; and a codex/agy shared-directory removal restoring the directory
exactly once in the active agent's format.

Targeted (tests/integrations/test_integration_subcommand.py,
tests/test_presets.py, tests/test_extensions.py,
tests/test_extension_skills.py,
tests/integrations/test_integration_opencode.py,
tests/integrations/test_integration_claude.py): 930 passed.
Full suite: 3930 passed, 109 skipped.
ruff check: clean on files touched by this change.

Refs #2948

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: guard skill subdirectories and active-agent scoping in preset reconciliation

Fix 4 issues from round-6 review of the active-only integration
registration work (#2948):

- remove(): removed_cmd_names only collected primary command names from
  registered_commands + manifest aliases, missing commands that were
  only ever registered via skills mode (ai_skills guard returns no
  command names for command-backed integrations in skills mode). This
  skipped reconciliation entirely when removing a higher-priority
  skills-mode preset, causing _unregister_skills() to fall back to
  core/extension content instead of the surviving lower-priority
  preset's override. Now every command template's primary name is
  added to removed_cmd_names unconditionally.

- _reconcile_composed_commands(): the "composed is None" branch (fires
  when no replace-strategy layer remains for a command, e.g. after
  removing a wrap/append preset's base) called unregister_commands()
  across every configured non-skill agent, ignoring only_agent. This
  deleted historical artifacts from integrations that were never active
  for the preset. Now filtered by only_agent like the rest of the file.

- Added _validate_skill_subdir() helper (reusing
  _ensure_safe_shared_directory/_validate_safe_shared_directory from
  shared_infra.py) and applied it at every site that reads or writes an
  individual skill subdirectory (_register_skills,
  _unregister_skills_in_dir, _reconcile_skills' override_skills
  restoration loop). _safe_skills_dir_for_agent only validated the
  parent skills directory; a symlinked leaf subdirectory (e.g.
  .claude/skills/speckit-specify) would slip past that check since
  is_dir()/exists() follow symlinks, letting write_text/rmtree operate
  through it to an arbitrary location outside the project.

Added regression tests: removing a higher-priority skills-only preset
restores the surviving lower-priority preset's content; composed-is-None
unregistration only touches the active agent; symlinked skill subdirectory
rejected on restore; symlinked skill subdirectory rejected on write.

Targeted (934) and full (3934 passed, 109 skipped) test suites and ruff
check pass clean.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: persist command registration before fallible skills phase on rescaffold

Fix remaining round-6 review findings on the active-only integration
registration work (#2948):

- register_enabled_presets_for_agent(): registered_commands and
  registered_skills were merged and persisted together in a single
  registry.update() call after both the commands and skills phases ran.
  If _register_skills() raised, the per-preset try/except swallowed it
  before that update() call was reached, even though _register_commands()
  had already written a real command file to disk. That file became
  untracked, so preset removal could no longer clean it up.
  install_from_directory() already persists registered_commands
  immediately after the commands phase, before starting the independently
  fallible skills phase; rescaffold now does the same.

- test_presets.py: renamed a misleading claude_dir variable (pointing at
  Gemini's command directory) in
  test_composed_none_unregister_respects_active_agent to reuse the
  existing gemini_commands_dir variable already defined earlier in the
  same test.

Added regression test
test_rescaffold_persists_commands_before_fallible_skills_phase:
simulates a skills-phase failure during rescaffold and asserts the
command file already written to disk is still tracked in
registered_commands.

Verified all other round-6 findings (preset active-integration scoping,
preset reconciliation/remove paths, skills-mode switching, override
precedence during rescaffold, skill-subdirectory symlink safety) are
already addressed by prior commits in this branch; re-checked each
against current code before concluding no further change was needed.

Targeted (tests/test_presets.py, tests/test_extensions.py: 689 passed)
and full (3935 passed, 109 skipped) suites and ruff check on changed
files pass clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: unregister stale opposite-mode preset artifact on same-agent skills toggle

Fix an Important gap in register_enabled_presets_for_agent() surfaced by
quality review (#2948): toggling ai_skills for the *same already-active*
command-backed agent (e.g. `integration upgrade copilot` after flipping
ai_skills, with copilot staying active throughout) left a stale artifact
from the previous mode behind, violating the command/skill mutual-
exclusion invariant this PR otherwise enforces.

- command -> skills: _register_commands()'s ai_skills guard makes the
  commands phase a no-op, but the previously-written command file (e.g.
  .agent.md) and its registered_commands[agent] entry were never cleaned
  up, so it lingered alongside the newly written SKILL.md.
- skills -> command: _get_skills_dir() stops resolving a skills directory
  once ai_skills is off, making the skills phase a no-op, but the
  previously-written SKILL.md and its registered_skills[agent] entry were
  never cleaned up, so it lingered alongside the newly (re)written command
  file.

register_enabled_presets_for_agent() now resolves once per call whether
agent_name is a command-backed integration (extension != "/SKILL.md") and
the current ai_skills state, then narrowly unregisters the stale opposite-
mode entry for that agent via the existing _unregister_commands /
_unregister_skills helpers before persisting updated tracking — mirroring
the same per-agent, per-preset isolation already used elsewhere in this
method. Native skill-only agents (claude, codex, ...) are unaffected:
they have no command/skill toggle, so registered_commands and
registered_skills legitimately co-exist for them by design. The trailing
reconciliation pass, project-override precedence, and per-preset
partial-failure isolation are all unchanged.

Added red-first regression tests exercising the real install +
register_enabled_presets_for_agent rescaffold path in both toggle
directions:
- test_rescaffold_toggle_command_to_skills_removes_stale_command_file
- test_rescaffold_toggle_skills_to_command_removes_stale_skill_file

Both failed against the prior code (stale artifact persisted / registry
still tracked it) and pass after the fix.

Targeted (tests/test_presets.py, tests/test_extensions.py: 691 passed)
and full (3937 passed, 109 skipped) suites and ruff check on changed
files pass clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: migrate legacy flat-list registered_skills on rescaffold even when unchanged

Fix a valid finding from GitHub Copilot's review of HEAD b9d9053 (#2948):
register_enabled_presets_for_agent() normalizes a legacy flat-list
registered_skills value (predating per-agent provenance) to the
{agent_name: [...]} dict shape in memory via _normalize_registered_skills,
but the persistence check only compared the two *normalized* forms. When
the freshly rescaffolded skill names are identical to what the legacy
list already held — the common case, since nothing about the preset or
skill actually changed — that comparison is a no-op and registry.update()
is skipped, leaving the *raw* on-disk value as the un-migrated flat list.

A later switch to a different skill-mode agent and removal then follows
_unregister_skills's legacy best-effort path (restore only the currently
active agent's directory) instead of the per-agent provenance path,
permanently orphaning the first agent's override.

Fix: track the raw (pre-normalization) existing value and force
persistence whenever it's a non-empty list, independent of whether the
normalized content changed. Traced registered_commands for the same
class of bug: its registry value has always been Dict[str, List[str]]
(no legacy flat-list format ever existed for it — the existing
`if not isinstance(existing_commands, dict): existing_commands = {}`
guard is not a lossy migration path), so this fix stays scoped to
registered_skills only.

Added red-first regression test
test_rescaffold_migrates_legacy_flat_list_registered_skills: installs a
preset, overwrites its registry entry with a raw legacy flat list,
rescaffolds the *same* active agent with unchanged skill names, and
asserts the raw registry is migrated to per-agent dict form. Extends the
scenario with a switch to a second skill-mode agent and preset removal
to prove both agents' directories restore cleanly instead of orphaning
the first. Failed against the prior code (raw value stayed a list) and
passes after the fix.

Targeted (tests/test_presets.py, tests/test_extensions.py: 692 passed)
and full (3938 passed, 109 skipped) suites and ruff check on changed
files pass clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: reconcile before fallible skills phase, infer legacy skill provenance, and unregister stale extension artifacts on toggle

Three findings from the Copilot review on HEAD b9d9053/3a1e749:

1. `register_enabled_presets_for_agent()` only recorded a preset's command
   names into `affected_cmd_names` (the set later passed to
   `_reconcile_composed_commands`/`_reconcile_skills`) in the loop that ran
   *after* `_register_skills()`, inside the same per-preset `try` block. If
   `_register_skills` raised, the `except` caught it and `continue`d before
   that loop ever ran — so a preset whose commands phase already wrote real
   content to disk never got reconciled against the full priority stack,
   leaving its raw content in place instead of a project override or
   higher-precedence preset's content. Fix: record the manifest's command
   names immediately after the commands phase succeeds and persists, before
   calling the independently fallible `_register_skills()`.

2. The legacy flat-list `registered_skills` migration (added for the
   previous review round) attributed every name in the list to whichever
   agent was currently being (re)activated. If the first operation after
   upgrading from a pre-#2948 registry was a direct switch to a *different*
   skill-mode agent (e.g. a legacy Claude override, then `integration use
   codex` with no intervening Claude rescaffold), the migrated dict only
   recorded `{"codex": [...]}`, permanently losing Claude's actual
   provenance and orphaning its override on later removal. Fix: added
   `_infer_legacy_skill_provenance()`, which probes every configured
   skill-mode agent's directory (via the same safe, symlink-validated
   helpers already used for restore/removal) for a `SKILL.md` whose
   frontmatter records this exact preset as the owner
   (`metadata.source == "preset:<pack_id>"`). A name found under more than
   one directory is attributed to every matching agent (the preset may have
   been active while the user switched between several skill-mode agents
   before provenance tracking existed); names that can't be matched to any
   directory still fall back to the previously-active best-effort
   behaviour. Directory grouping for shared-path aliases (e.g.
   agy/codex/zed all resolving to `.agents/skills`) intentionally does not
   call `.resolve()` on the path, since doing so diverges from
   `project_root`'s own resolution state on platforms where a path
   component is itself a symlink (e.g. macOS's `/var` -> `/private/var`)
   and made every subsequent containment check spuriously fail.

3. `register_enabled_extensions_for_agent()` has the same command/skill
   mutual-exclusion gap the preset path had (fixed in a previous round):
   toggling `ai_skills` for the *same active* agent left the opposite
   mode's artifact behind. Command -> skills left the extension's
   `.agent.md` file and its `registered_commands[agent]` entry in place
   once `skills_mode_active` made the commands phase a no-op. Skills ->
   command left the extension's `SKILL.md` file in place, since an empty
   `_register_extension_skills()` result (because this agent's skills
   directory no longer resolves once `ai_skills` is off) was treated as
   "nothing to register" rather than "this was rendered here before and is
   now stale". This diverges from the preset path in one respect:
   `registered_skills` for extensions has always been a flat list with no
   per-agent provenance (extension skills are only ever rendered for the
   active agent, never per-preset-per-agent tracked), so the fix resolves
   ownership by checking which of the extension's tracked skill names
   still exist as directories under this specific agent's directory before
   removing them — mirroring the same technique `unregister_agent_artifacts`
   already uses for full agent deactivation, but scoped narrowly to firing
   only when a toggle is actually detected (`skills_mode_active` /
   `command_mode_active`), so a same-mode re-run never disturbs
   already-correct artifacts or a user's manual customizations.

Regression tests (all confirmed red before their respective fix, green
after):
- tests/test_presets.py::TestPresetSkills::test_rescaffold_reconciles_override_even_when_skills_phase_fails
- tests/test_presets.py::TestPresetSkills::test_rescaffold_legacy_flat_list_direct_switch_preserves_original_agent
- tests/test_extension_skills.py::TestExtensionSkillRegistration::test_rescaffold_toggle_command_to_skills_removes_stale_extension_command_file
- tests/test_extension_skills.py::TestExtensionSkillRegistration::test_rescaffold_toggle_skills_to_command_removes_stale_extension_skill_file

Verification: tests/test_presets.py + tests/test_extensions.py +
tests/test_extension_skills.py (753 passed), tests/integrations/ (1768
passed, 1 skipped), full suite `pytest tests -q` (3942 passed, 109
skipped), `ruff check` on changed files clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: broaden legacy skill provenance inference to command-backed agents

_infer_legacy_skill_provenance() only probed agents whose registrar
config statically declares extension == "/SKILL.md", excluding
command-backed agents (e.g. Copilot) that can also render preset
overrides as SKILL.md files when ai_skills is enabled. A real
preset-owned .github/skills/.../SKILL.md written while Copilot was the
active skills-mode agent was therefore never probed and got
misattributed entirely to whichever agent activated first after the
upgrade, permanently orphaning Copilot's override on later removal.

Broaden the candidate set to every configured integration
(CommandRegistrar.AGENT_CONFIGS), reusing the existing safe-path
helper (_safe_skills_dir_for_agent, itself built on the shared
_get_skills_dir resolver) rather than inventing new path-construction
logic. The existing preset-marker match (metadata.source ==
"preset:<pack_id>") continues to gate every attribution, so
command-mode agents that never rendered this preset's skill are not
falsely attributed.

Add red-first regression tests: a legacy flat-list entry owned by
Copilot in skills mode, switched directly to Claude with no
intervening Copilot rescaffold, now migrates to a per-agent dict
covering both agents, and removal restores both agents' files instead
of orphaning Copilot's override; plus a negative-case test confirming
a command-mode Copilot with no preset-owned skill marker is not
falsely attributed during the same migration.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: preserve extension skill tracking for mirrors in other agent dirs

The skills -> command toggle cleanup in
register_enabled_extensions_for_agent() recomputed the remaining
tracked registered_skills names by checking only the toggling agent's
own skills directory. Since registered_skills is a single flat list
shared across every agent an extension has ever been activated under
(skills are only ever rendered for the active agent, so there is no
per-agent registry key), a name whose mirror still existed under a
*different*, previously-active agent's directory was incorrectly
dropped from tracking as soon as the current agent's own copy was
removed. A later full removal only iterates registered_skills, so the
orphaned mirror under the other agent's directory was never found or
cleaned up.

Add _extension_owned_skill_names(), which re-verifies ownership across
every configured agent's skills directory (deduped by shared path) the
same way the existing _unregister_extension_skills() fallback scan
already does, keeping a name only when a SKILL.md with a matching
metadata.source == "extension:<id>" marker is found somewhere -
read-only, no directory creation, no symlink escape. Use it instead of
re-checking only the toggling agent's own directory when recomputing
what remains tracked after narrow stale-mirror cleanup.

Add a red-first regression test: Auggie is activated in skills mode
first (writing a mirror), then Copilot is activated in skills mode
(writing its own mirror for the same names), then Copilot toggles to
command mode. Before the fix, registered_skills lost both names
entirely even though Auggie's mirrors were untouched on disk; after
the fix tracking is preserved and a subsequent full removal correctly
cleans up Auggie's remaining mirrors too.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: reject symlinked skills-directory escape in extension skill scans

_extension_owned_skill_names() and the fast/fallback paths of its
sibling _unregister_extension_skills() called skills_candidate.resolve()
and then checked children relative to that already-resolved candidate.
If the candidate directory itself (e.g. .gemini/skills) was a symlink
pointing outside the project root, both the resolve() call and the
subsequent containment check silently passed through the symlink
instead of rejecting it:

- _extension_owned_skill_names() would falsely attribute ownership to
  a marker-matching SKILL.md living outside the project.
- _unregister_extension_skills()'s fast path (an explicit skills_dir,
  as passed by the toggle-cleanup call site) and its fallback scan
  (used during full extension removal) would both shutil.rmtree() the
  external directory, deleting unrelated content outside the project.

Fix by validating the candidate directory itself with the existing
_validate_safe_shared_directory() shared-infra helper before any probe
or delete: it rejects a symlink at any path component (walking down
from the project root, including the final component) without ever
resolving through it, and is already used elsewhere in the codebase for
the same class of shared-directory containment check. Unsafe
candidates are skipped/refused rather than followed.

Add red-first security regression tests reproducing each of the three
call sites with a `.gemini/skills` symlink pointing at an external
directory containing a marker-matching SKILL.md and an unrelated
precious_file.txt: provenance inference must not attribute the name,
and both the explicit-skills_dir fast path and the None-skills_dir
fallback scan must leave the external directory and file untouched.
Existing valid shared/deduped directory tests (e.g. agy/amp/codex/zed
sharing .agents/skills) continue to pass, confirming legitimate shared
directories still clean up correctly.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix unscoped extension-skill removal and legacy preset provenance on direct remove

- _unregister_extension_skills(): omitting skills_dir now always triggers
  the full multi-directory fallback scan instead of narrowing to the
  currently active agent's directory. Previously, remove() (the only
  caller that omits skills_dir) would resolve the active agent's dir and
  take the scoped fast path, orphaning a previously-active second agent's
  extension skill mirror during full removal.

- PresetManager.remove(): infer legacy flat-list registered_skills
  provenance (reusing _infer_legacy_skill_provenance from the prior
  rescaffold fix) before invoking _unregister_skills, so a direct
  `preset remove` with no intervening rescaffold/switch also restores
  every previously-active agent's directory instead of only the
  currently active one.

Added regression tests:
- test_remove_while_second_agent_still_in_skills_mode_cleans_up_first_agent_mirror
- test_remove_infers_legacy_flat_list_provenance_without_prior_rescaffold

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Keep unregister_agent_artifacts scoped to its agent when directory is absent

ExtensionManager.unregister_agent_artifacts() converted its resolved
agent_skills_dir to None whenever that directory didn't exist, before
calling _unregister_extension_skills(). After 1d8f9e3, omitting
skills_dir means "genuinely unscoped removal": scan every configured
agent's directory, reserved for ExtensionManager.remove()'s full
project cleanup. Since unregister_agent_artifacts is agent-scoped (used
by switch to clean up the previous integration's artifacts), this
caused it to delete every other agent's live extension skill mirrors
whenever the target agent's own directory happened to be absent, e.g.
unregistering an agent that was never activated.

Fix: always pass the explicit, agent-scoped skills_dir, even when it
doesn't exist on disk, so the fast path is a safe no-op for an absent
directory instead of falling back to the all-agents scan. Registry
reconciliation (dropping removed names from the flat registered_skills
list) now only runs when the agent's directory actually exists, so an
absent directory can't be misread as "these names were removed
everywhere" and wipe tracking for mirrors that still legitimately live
under other agents' directories.

Added regression test:
- test_unregister_agent_artifacts_stays_scoped_when_agent_dir_absent

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Preserve global skill tracking across agents in unregister_agent_artifacts

The present-directory branch of ExtensionManager.unregister_agent_artifacts()
recomputed "remaining" registered_skills only by checking whether each name
still existed under the just-cleaned agent's own directory. registered_skills
is a single flat list shared across every agent an extension was ever
activated under (skills are only ever rendered for the currently active
agent, so there's no per-agent registry key). Repro: auggie and copilot both
have mirrors for the same extension; unregister_agent_artifacts("auggie")
correctly removes auggie's own mirror, sees the names absent from auggie's
(now empty) directory, and stores an empty registered_skills list - even
though copilot's mirror is still live on disk and now untracked. A later full
remove() then reads an empty registry and leaves copilot's mirror orphaned.

Fix: after the agent-scoped cleanup, recompute remaining names with
_extension_owned_skill_names(), which scans every safe, configured agent
skills directory (not just the one just cleaned) and keeps a name only if a
marker-verified SKILL.md for this extension still exists somewhere. This is
the same helper already used for the analogous same-agent toggle-cleanup
case, so no new abstraction was introduced. Explicit per-agent cleanup,
marker ownership verification, and symlink/containment safety are unchanged.

Added regression test:
- test_unregister_agent_artifacts_preserves_tracking_for_other_agent_mirror

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Reconcile every historical agent on preset removal; validate child skill dirs

Fixes 3 findings from the Copilot review on HEAD 31c9b97 (#2948):

1. presets/__init__.py: remove()'s command reconciliation only recreated
   the surviving preset's content for the currently active agent, even
   though the removed preset's registered_commands could span multiple
   historical (now-inactive) agents recorded via prior rescaffolds. Now
   remove() captures every historical agent registered_commands actually
   targeted (before mutation) and passes it as extra_agents through
   _reconcile_composed_commands -> _register_for_non_skill_agents /
   _register_command_from_path -> registrar.register_commands_for_non_
   skill_agents, so the active-only restriction for install/use is
   preserved while post-removal reconciliation restores every touched
   directory.

2. presets/__init__.py: the analogous gap existed for skills. _unregister_
   skills() now returns {skills_dir: renderer_agent} for every directory it
   actually restored, and _reconcile_skills() accepts extra_skills_dirs to
   reconcile each of those directories (via a new apply_to_dir() helper),
   not only the currently active skills directory. _register_skills() gained
   optional target_dir/target_agent overrides (forcing
   create_missing_skills off for non-active directories) so a historical
   directory is only ever restored, never seeded with brand-new skills.

3. extensions/__init__.py: _extension_owned_skill_names() and both the
   fast and fallback paths of _unregister_extension_skills() validated only
   the parent skills_dir for symlink escape, then resolved
   skills_dir / skill_name and checked containment relative to that
   already-resolved parent. A per-skill child that is itself a symlink to
   a different, legitimate skill directory within the same (safe) root
   passed that containment check, so deleting/attributing through the
   symlink name could destroy or misattribute an unrelated skill reached
   only via the alias. All three call sites now run the shared
   _validate_safe_shared_directory() component-wise check against the full
   skills_dir / skill_name path (not just the parent) before any read or
   delete, rejecting a symlinked child outright rather than following it,
   even when its resolved target remains in-bounds.

Regression tests added (all confirmed red against pre-fix code, green
after):
- test_remove_reconciles_command_for_every_historical_agent
- test_remove_reconciles_skill_for_every_historical_agent
- test_extension_owned_skill_names_rejects_symlinked_child_skill_dir
- test_unregister_extension_skills_explicit_dir_rejects_symlinked_child
- test_unregister_extension_skills_fallback_rejects_symlinked_child

Tests: tests/test_presets.py (361), tests/test_extension_skills.py (69),
tests/test_extensions.py (338) all pass; tests/integrations (1768 passed,
1 skipped) pass; full suite 3902 passed / 74 skipped (90 pre-existing,
environment-only git-signing tests deselected — confirmed failing
identically on the pre-change baseline due to local 1Password SSH-agent
signing, unrelated to this change). ruff check clean on all changed files.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Persist historical reconciliation ownership; defer destructive toggle cleanup; validate registry-provided skill names

Round 11 review findings (5 comments on HEAD ab6c28c), three root causes:

A) Historical-agent reconciliation wrote surviving content to disk but
   discarded the returned per-agent write map, so the preset's own
   registered_commands/registered_skills never learned about directories
   reconciliation restored on its behalf. A later removal of that same
   preset then orphaned those directories. Added
   _merge_pack_registered_commands/_merge_pack_registered_skills and wired
   them into _reconcile_composed_commands and _reconcile_skills's
   apply_to_dir so every actual write is merged back into the winning
   preset's registry metadata.

B) Command<->skills toggle on an already-active agent deleted the old
   artifact before the replacement registration ran, in both
   presets/__init__.py's register_enabled_presets_for_agent and
   extensions/__init__.py's register_enabled_extensions_for_agent. If the
   replacement step raised, both artifacts were lost. Deferred the
   destructive cleanup until after the replacement phase completes
   without raising (register-new-then-remove-old ordering); the mirror
   skills->command direction was already safe since the new command file
   is always registered unconditionally before any cleanup runs.

C) _unregister_skills_in_dir and _infer_legacy_skill_provenance joined a
   registry-provided (untrusted) skill name directly onto a directory
   before any name-shape validation. An absolute in-project name discards
   the intended parent directory entirely (Path's "/" operator drops the
   left side for an absolute right side), letting a corrupted registry
   entry escape the intended skills subtree while still resolving inside
   the project root - passing the existing containment/symlink check.
   Added a centralized _is_safe_registry_skill_name guard (rejecting
   non-strings, empty strings, absolute paths, multi-component paths, and
   "."/".." ) and applied it before every path join derived from
   registry-provided skill names in both functions. Also fixed
   _infer_legacy_skill_provenance's unmatched-name fallback, which
   previously still attributed rejected names to fallback_agent even
   after the loop skipped them.

Added red-first regressions for all three root causes, covering: a
two-preset historical-command-agent survivor scenario, an analogous
skill-agent survivor scenario, injected skills-phase failure during a
preset command->skills toggle and the extension equivalent, a direct
unit test of the new name-safety guard, an absolute-path escape attempt
against _unregister_skills_in_dir, and a false-attribution attempt
against _infer_legacy_skill_provenance.

Tests: tests/test_presets.py (367 passed), tests/test_extension_skills.py
+ tests/test_extensions.py (408 passed), tests/integrations (1768
passed, 1 skipped), full suite tests -q deselecting the pre-existing
1Password-signing-affected tests/extensions/git/test_git_extension.py
(3909 passed, 74 skipped, 90 deselected). ruff check clean on all
changed files.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Verify replacement actually landed before retiring stale toggle artifacts

The command<->skills toggle cleanup added for #2948 deferred destructive
removal of the old-mode artifact until after the replacement registration
call completed without raising. That was necessary but not sufficient:
none of _register_skills(), _register_commands(),
register_commands_for_agent(), or _register_extension_skills() raise on
a missing source template, a safety-validation skip, or a corrupted
manifest entry — they simply return an empty or partial result. Treating
"did not raise" as "fully replaced" meant a stale artifact could still be
deleted (or its tracking dropped) even though its specific replacement
never actually landed, leaving neither artifact in place for that logical
command/skill.

Fix all four affected toggle directions by checking the replacement
call's actual return value before allowing any destructive step:

- presets command->skills (register_enabled_presets_for_agent): only
  unregister a stale command name once its corresponding skill name
  (via the existing _skill_names_for_command() helper) is confirmed
  present in the skills call's returned names for that agent; the
  remainder stays tracked and on disk.
- presets skills->command (register_enabled_presets_for_agent): only
  unregister a stale skill name once its corresponding command name is
  confirmed present in the commands call's returned names for that
  agent, using the same helper.
- extensions skills->command (register_enabled_extensions_for_agent):
  only remove a skill mirror once the matching command (mapped via the
  existing HookExecutor._skill_name_from_command() helper) is confirmed
  present in register_commands_for_agent's returned names.
- extensions command->skills (register_enabled_extensions_for_agent):
  only remove a deferred stale command once its matching skill name is
  confirmed present in _register_extension_skills()'s returned names.

All four reuse the existing command<->skill name-derivation helpers
rather than inventing new mapping logic. Registry tracking is updated to
retain exactly the unreplaced subset rather than being popped wholesale,
so partially-successful toggles leave correct, minimal tracking behind.

Added 8 new regression tests (4 presets, 4 extensions) covering both the
fully-empty and genuinely-partial result cases for each of the four
toggle directions, using real missing-source-file scenarios (not mocked
return values) to exercise the actual code paths. Confirmed red before
the fix and green after for all 8.

Focused (test_presets.py, test_extension_skills.py, test_extensions.py,
tests/integrations): 2551 passed, 1 skipped.
Full suite (tests, excluding the pre-existing environment-local
1Password-signing git-extension failures): 3917 passed, 74 skipped, 90
deselected.
ruff check: clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Retire alias command groups on toggle; scope preset cleanup to switched-away agent (#2948)

Fixes three current Copilot review findings on HEAD d0d152e:

1. Command->skills toggle cleanup only matched a stale command's own
   name against the returned replacement skill name. Aliases
   (CommandRegistrar tracks and returns primary + alias names flattened
   into one list) never have their own skill rendered -- only the
   primary command's skill is rendered -- so an alias's name could never
   match, leaving its command artifact and tracking behind forever even
   after the primary's replacement landed. Fixed identically in both
   presets (register_enabled_presets_for_agent) and extensions
   (register_enabled_extensions_for_agent): build a primary->alias
   mapping from the manifest, group stale names by primary, and
   retire/keep the whole group together based solely on whether the
   primary's skill replacement actually landed.

2. `integration switch` to a not-yet-installed target unregistered the
   old agent's extension artifacts but had no preset equivalent, so a
   preset's command overrides (including custom preset commands) and
   skill mirrors for the deactivated agent lingered as orphans. Added
   `PresetManager.unregister_agent_artifacts()`, mirroring
   `ExtensionManager.unregister_agent_artifacts()`: scoped strictly to
   the given agent, migrates a legacy flat-list `registered_skills`
   entry via existing on-disk provenance inference before removing
   anything (so other agents' real ownership is preserved rather than
   guessed or dropped), and guards against double-processing an
   artifact through both the commands and skills paths for native
   SKILL.md agents. Wired via a new `_unregister_presets_for_agent()`
   helper into the integration switch command's existing old-agent
   cleanup phase.

Added red-first regression tests:
- tests/test_presets.py: alias-group retire/keep/partial-multi-group
  tests for the command->skills toggle; unregister_agent_artifacts
  scoping tests for commands and legacy-list skill provenance.
- tests/test_extension_skills.py: alias-group retire/keep tests for the
  extension command->skills toggle.
- tests/integrations/test_integration_subcommand.py: end-to-end switch
  test proving a preset's custom command override is cleaned up when
  switching to a not-yet-installed integration, with tracking updated
  correctly and the new agent's registration unaffected.

All new tests confirmed red (AttributeError / orphaned file assertions)
before the fix and green after. Full suite: 3980 passed, 109 skipped.
ruff check clean on all changed files.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: track reconciled extension artifacts

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix native skill preset reconciliation

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix shared native skill cleanup

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix partial preset rescaffold tracking

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix preset agent skill lifecycle

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Clarify preset removal reconciliation

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(integrations): address upgrade review feedback

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): reconcile partial command writes

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address active artifact cleanup review

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: defer preset skill cleanup to winning command

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: track reconciled and partial preset skills

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: reconcile project overrides to legacy skills

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: harden preset skill writes and rollback

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): harden legacy skill restoration

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): preserve non-owned legacy skills

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: validate reconciled skill paths

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): preserve reconciled skill ownership

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): clean reconciled agent skills

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: keep legacy cleanup project-local

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): keep active agent's artifacts in its current mode on remove

A partially failed command<->skills toggle leaves stale tracking
(registered_commands or registered_skills) for the active agent, and
remove() replayed that history regardless of the agent's current mode:

- extra_agents re-admitted the active skills-mode agent into command
  reconciliation, recreating its command file from a surviving lower
  preset even though only_agent excluded it.
- _unregister_skills restored (and _reconcile_skills reapplied) a skill
  artifact for the active command-mode agent instead of deleting the
  preset-owned leftover.

The active agent's participation is now decided exclusively by its
current mode: reconciliation strips it from extra_agents, and removal
routes its stale skills through _delete_agent_preset_skills. Historical
replay still applies to inactive agents only (#2948).

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: filter uninstalled-extension commands in reconciliation; allow active-agent layout change with presets

Two follow-ups to the upstream-main merge:

- Preset reconciliation (_reconcile_composed_commands) now skips
  extension-scoped commands (speckit.<ext>.<cmd>) whose extension is not
  installed, at the single chokepoint every install/remove/rescaffold
  pass funnels through. Registration already refused them, so
  reconciliation could materialize files no registry entry tracks. The
  duplicated per-call-site filters collapse into one
  _extension_installed_for_command helper.

- The #3415 layout-change guard predates this PR's agent-scoped preset
  rescaffold: for the active integration, _register_presets_for_agent
  now re-registers enabled presets in the new layout and retires the
  old layout's stale files, so an active-agent command<->skills toggle
  proceeds and reconciles instead of being rejected. The guard still
  rejects non-active agents (no rescaffold runs for them) and still
  fails closed on an unreadable registry.
  _installed_presets_affecting_agent also understands the per-agent
  dict shape of registered_skills this PR writes, instead of raising
  'malformed'.

Regression tests: rescaffold with an uninstalled extension's command,
CLI-level legacy<->skills toggle with an installed preset (both
directions), secondary-agent rejection, and dict-shaped
registered_skills in the guard helper.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: reject active layout change while a disabled preset owns artifacts

The post-upgrade preset rescaffold iterates enabled presets only, and a
disabled preset's artifacts are deliberately frozen until removal, so an
active-agent command<->skills layout change cannot reconcile them.
_installed_presets_affecting_agent now reports each preset's enabled
state and the guard rejects the migration while any affected preset is
disabled, with re-enable/remove guidance. Enabled presets and non-active
rejection behave as before.

Regression test: disabled preset blocks the toggle untouched; re-enabling
unblocks it and reconciles.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs: replace placeholder prefix in two safety comments

Comment-only: spell out why skill deletion is restricted to
project-local directories (flat/legacy provenance cannot prove
home-directory ownership) instead of an undefined placeholder word.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs: correct guard-helper docstring to active-only registration model

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: fail closed on non-list values in per-agent preset provenance

A dict-shaped registered_skills/registered_commands entry with a
non-list value (e.g. null) left ownership undecidable but read as "no
artifacts", letting a layout-changing upgrade proceed on a malformed
registry. Validate values are lists and raise
_PresetRegistryUnreadableError otherwise, matching the guard's
fail-closed contract. Unit test covers both fields.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: drop eager extension unregister on layout-changing upgrade

Unregistering the agent's extension artifacts before re-registration
deleted files and registry tracking up front, so a failed or partial
re-registration left the extension with no artifacts at all. Retirement
of each opposite-mode artifact already belongs to
register_enabled_extensions_for_agent's deferred toggle cleanup, which
removes an old artifact only after its replacement is confirmed. Also
keeps disabled extensions consistent with disabled presets: artifacts
stay frozen in place with intact tracking.

Regression test corrupts the installed extension manifest so
re-registration fails, then asserts the old-layout artifacts and their
registry tracking survive the upgrade.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: rescaffold fallback integration after failed switch rollback

When Phase 2 of a switch fails, rollback restores another installed
integration as the default via _set_default_integration but never
re-registered extensions or presets for it. Under active-only
registration the fallback may never have received any artifacts (it
was installed while another integration was active), and Phase 1
already unregistered the outgoing agent's artifacts — leaving the
restored default unusable. Rescaffold both extensions and presets
(best-effort) after the fallback default is successfully restored.

Regression test: secondary codex install with the git extension, a
failing switch to generic, then asserts codex ends up with registered
extension artifacts after rollback.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs: explain load-bearing pre-create loop in _reconcile_skills

The per-skill _validate_skill_subdir(create=True) loop looks like dead
code (its result is unused), but it re-creates the tracked skill
subdirectories that _unregister_skills just deleted so
_register_skills's only-overwrite-existing gate passes during a
historical-directory restore. Removing it fails
test_skill_reconciliation_preserves_per_directory_names.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: preserve dashed-description skill tracking

Use the shared frontmatter parser when verifying surviving extension skill mirrors so delimiter substrings cannot hide provenance metadata.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: skip absent extension skills during reconciliation

Filter extension-scoped commands before skill reconciliation so historical preset tracking and project overrides cannot recreate artifacts for uninstalled extensions.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: preserve partial native skill cleanup

Coordinate native-skill command cleanup with registered skill coverage per agent and command so partial rescaffolds cannot orphan preset artifacts.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-27 14:09:40 -05:00
github-actions[bot]
3ca0eb169e Add Intake Sequencing Governance preset to community catalog (#3761) 
Add intake-sequencing-governance preset submitted by @hindermath to:
- presets/catalog.community.json (alphabetical order)
- docs/community/presets.md community presets table

Closes #3742

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-27 08:16:57 -05:00
github-actions[bot]
eb8108e7b3 Update Verify Review Ship extension to v0.4.1 (#3759) 
Update verify-review-ship extension submitted by @cadugevaerd to:
- extensions/catalog.community.json (version, download_url, sha256, description, requires, provides, tags, updated_at)
- docs/community/extensions.md community extensions table

Closes #3751

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-27 08:00:08 -05:00
github-actions[bot]
ae0b8ca2b0 Update Intake Review Governance preset to v0.1.1 (#3729) 
Update intake-review-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description)
- docs/community/presets.md community presets table

Closes #3727


Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-24 15:33:14 -05:00
github-actions[bot]
2fe35bf898 Update Verify Review Ship extension to v0.3.0 (#3728) 
Update verify-review-ship extension submitted by @cadugevaerd:
- extensions/catalog.community.json (version, download_url, description, effect, tags, sha256, updated_at)
- docs/community/extensions.md community extensions table

Closes #3726

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-24 15:28:25 -05:00
Ali jawwad
ffe2a7ffd6 docs(upgrade): Claude Code files live in .claude/skills, not .claude/commands (#3708) 
The Claude Code integration installs skills into `.claude/skills` (see
integrations/claude: `"dir": ".claude/skills"`), and the "what gets kept"
list earlier in this same doc already says `.claude/skills/`. But three
troubleshooting/reference spots still point users at `.claude/commands/`,
which does not exist for a Claude Code install -- so the "verify files
exist" checks list an empty/missing directory. Correct all three to
`.claude/skills/`.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-07-24 11:51:40 -05:00
WOLIKIMCHENG
ae82c74339 fix(kilocode): install commands under .kilo/commands (#3672) 
* fix(kilocode): write commands to .kilo/commands

* fix: guard Kilo legacy command migration

---------

Co-authored-by: root <kinsonnee@gmail.com>
 2026-07-24 11:05:32 -05:00
github-actions[bot]
b0850c97e6 Update Intake Authoring Governance preset to v0.2.0 (#3721) 
Update intake-authoring-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, provides, tags)
- docs/community/presets.md community presets table

Closes #3720


Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-24 10:51:23 -05:00
Manfred Riem
781a14a6d2 docs: clarify shell-step interpolation safety (#3719) 
* docs: clarify shell-step interpolation safety

Shell step `run` fields are executed by the system shell and `{{ ... }}`
expressions are substituted as raw, unquoted text. Document that untrusted
sources — workflow `inputs.*` and prior-step output, including AI-generated
`prompt` output — must be quoted, enum-constrained, validated, or gated before
they reach a `run` field.

- docs/reference/workflows.md: add an "Interpolation and shell safety" section.
- workflows/README.md: add a warning under the Shell Steps example, link to the
  new section, and quote the `inputs.project_dir` example.
- workflows/PUBLISHING.md: strengthen the interpolation guidance and call out
  prior-step/agent output as untrusted.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c0fd6900-69bf-4fcb-b377-de37f98f5835

* docs: correct shell-step interpolation guidance

Address review feedback that the previous wording over-promised. Clarify that
none of the mitigations neutralise a hostile interpolated value:

- Quoting is not a security boundary — there is no shell-escaping filter, and a
  value containing the matching quote can break out. Present quoting as
  correctness handling for already-constrained values only.
- Remove the "pass data via environment or files" guidance: ShellStep has no
  `env` mapping (it only copies the process environment and sets
  SPECKIT_WORKFLOW_DIR), so that transport does not exist.
- Drop the claim that routing through a command/prompt step validates or safely
  binds a value; it does not.
- Correct the gate guidance: a gate renders only its own message/show_file and
  does not inspect, resolve, or sanitise the following step. Authors must
  surface the exact command/data in the gate themselves, and approval does not
  neutralise an injectable interpolation.

Frame constraining values at the source (enum/allowlist) as the only reliable
control, and keeping unconstrained values out of `run` fields entirely.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c0fd6900-69bf-4fcb-b377-de37f98f5835

* docs: remove unsafe interpolation from example and gate guidance

Address further review feedback:

- workflows/README.md: the shell example interpolated an unconstrained path
  into shell source, which contradicted the warning beneath it. Shell steps
  already run from the project root, so drop the `cd '{{ inputs.project_dir }}'`
  prefix and model a plain `run: "npm test"` with no interpolation.
- docs/reference/workflows.md: GateStep prints `message` verbatim with no
  control-character stripping (stripping applies only to `show_file` path and
  contents), so recommending that authors surface untrusted data in `message`
  was itself unsafe — agent/caller output could inject terminal escapes to
  alter or hide the prompt. Direct authors to keep `message` to trusted text
  and surface untrusted material via `show_file`, whose contents are stripped.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c0fd6900-69bf-4fcb-b377-de37f98f5835

* docs: use correct prompt-step output key in example

A `prompt` step stores agent-generated text under `output.stdout`, not
`output.value`, so the example expression `{{ steps.plan.output.value }}`
would resolve to None. Reference `output.stdout` so the example correctly
demonstrates untrusted agent output flowing into a shell step.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c0fd6900-69bf-4fcb-b377-de37f98f5835

---------

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c0fd6900-69bf-4fcb-b377-de37f98f5835
 2026-07-24 10:40:26 -05:00
github-actions[bot]
be0c741ebb [extension] Add Blueprint Index — Living Architecture Map extension to community catalog (#3718) 
* Add Blueprint Index extension to community catalog

Add blueprint-index extension submitted by @ogil109 to:
- extensions/catalog.community.json (alphabetical order)
- docs/community/extensions.md community extensions table

Closes #3628

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
 2026-07-24 10:24:19 -05:00
Ali jawwad
391cc0dff8 fix(integrations): declare PiIntegration multi_install_safe (#3652) 
* fix(integrations): declare PiIntegration multi_install_safe

PiIntegration writes only to its isolated, static root .pi/prompts,
disjoint from every other integration, yet never declared
multi_install_safe — so it inherited the IntegrationBase default False,
leaving `specify integration status` in a permanent unsafe-multi-install
ERROR state when pi is co-installed alongside another agent.

Add `multi_install_safe = True`, mirroring the isolated MarkdownIntegration
cohort (qwen, shai, qodercli) and the kiro-cli #3471 fix. The parametrized
registry isolation contracts auto-include pi and pass.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs(integrations): list pi in the multi-install-safe reference table

Declaring PiIntegration multi_install_safe means the reference table in
docs/reference/integrations.md (which states it lists all currently
declared multi-install-safe integrations) should include it. Add the
alphabetized pi row with its .pi/prompts isolation path.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-07-24 09:48:30 -05:00
github-actions[bot]
58f5730dd5 Update Agent Parity Governance preset to v0.4.0 (#3697) 
Update agent-parity-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, description, documentation, updated_at)
- docs/community/presets.md community presets table

Closes #3684

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-23 15:09:31 -05:00
github-actions[bot]
579579ba80 [preset] Update Cross-Platform Governance preset to v0.2.1 (#3695) 
* Update Cross-Platform Governance preset to v0.2.1

Update cross-platform-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, updated_at)
- docs/community/presets.md community presets table

Closes #3683

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* ci: pin ruff to 0.15.0 to avoid 0.16.0 default-ruleset breakage

ruff 0.16.0 expanded its default rule set from ~59 to ~413 rules,
causing the unpinned `uvx ruff check` step to report 1476 pre-existing
violations. Pin to 0.15.0 to restore green lint until the codebase is
audited against the new defaults.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
 2026-07-23 14:38:40 -05:00
github-actions[bot]
34a086940f Update A11Y Governance preset to v0.4.1 (#3693) 
Update a11y-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, updated_at)
- docs/community/presets.md community presets table

Closes #3682

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-23 13:53:52 -05:00
github-actions[bot]
5ad312863f Update iSAQB Architecture Governance preset to v0.2.1 (#3687) 
Update isaqb-architecture-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, description, documentation, updated_at)
- docs/community/presets.md community presets table

Closes #3681

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-23 12:58:58 -05:00
github-actions[bot]
e14561f773 Update Architecture Governance preset to v0.5.1 (#3686) 
Update architecture-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, documentation, description, updated_at)
- docs/community/presets.md community presets table

Closes #3680

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-23 12:14:28 -05:00
github-actions[bot]
9b3546f437 Update Security Governance preset to v0.6.1 (#3685) 
Update security-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, description, documentation, updated_at)
- docs/community/presets.md community presets table

Closes #3679

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-23 11:08:26 -05:00
Ali jawwad
e9dfe900f6 fix(integrations): declare OmpIntegration multi_install_safe (#3650) 
* fix(integrations): declare OmpIntegration multi_install_safe

OmpIntegration is a plain MarkdownIntegration whose files live only under
its isolated, static root .omp/commands/, disjoint from every other
integration. But it never declared multi_install_safe, so it inherited the
IntegrationBase default False — leaving `specify integration status` in a
permanent unsafe-multi-install ERROR state whenever omp is co-installed
alongside another agent, with no acknowledgment path.

Add `multi_install_safe = True`, mirroring the isolated MarkdownIntegration
cohort (qwen, shai, qodercli, junie, kilocode) and the kiro-cli #3471 fix.
The parametrized registry isolation contracts auto-include omp once the flag
is set and pass (.omp/commands is isolated and its manifest disjoint).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs(integrations): list omp in the multi-install-safe reference table

Declaring OmpIntegration multi_install_safe means the reference table in
docs/reference/integrations.md (which states it lists all currently
declared multi-install-safe integrations) should include it. Add the
alphabetized omp row with its .omp/commands isolation path.

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Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-07-23 11:07:40 -05:00
github-actions[bot]
8def197612 Update Intake Authoring Governance preset to v0.1.1 (#3678) 
Update intake-authoring-governance preset submitted by @hindermath:
- presets/catalog.community.json (version, download_url, documentation, description, tags, updated_at)
- docs/community/presets.md community presets table

Closes #3676

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 2026-07-23 09:21:36 -05:00
Manfred Riem
7cd97e47f0 docs: add spec-kit-copilot to community friends (#3675) 
* docs: add spec-kit-copilot to community friends

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: c4ad8a5e-3ddb-44b2-b8ec-4f438c636b61

* docs: note first-party exception for spec-kit-copilot

Clarify the page disclaimer so it covers first-party GitHub projects, and
mark spec-kit-copilot as a first-party GitHub project.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

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---------

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Copilot-Session: c4ad8a5e-3ddb-44b2-b8ec-4f438c636b61
 2026-07-23 08:50:33 -05:00
Quratulain-bilal
e4cfa4c19c fix(integrations): declare kiro-cli multi-install safe (#3477) 
* tidy kiro-cli multi-install-safe declaration + add docs row and test

kiro-cli is declared multi_install_safe (it uses a fully isolated .kiro/
root, .kiro/prompts command dir, a stable '.' separator, and a dedicated
manifest — #3471). main ended up with the flag assigned twice in the class
body; this drops the bare duplicate and keeps a single declaration with the
comment explaining why it's safe.

also adds the missing kiro-cli row to the multi-install-safe table in
docs/reference/integrations.md, and a test asserting the flag is set (the
registry contract tests already enforce the actual path isolation against
every other safe integration).

* address review: drop agent-file column and duplicate test

per maintainer guidance on #3477: the Isolation table listed each
integration's agent-context file (AGENTS.md, CLAUDE.md, etc.) alongside
its command dir, which contradicted the safety definition (Copilot flagged
kiro-cli/codex both mapping to AGENTS.md). those context files are owned by
the optional agent-context extension, not by multi_install_safe — the flag
governs only the command directory + manifest.

- renamed the column to 'Command directory' and removed the agent-file
  entries, so it lists only what each integration actually manages
- reworded the definition to note agent-context is a separate concern and
  is not multi-install safe
- removed the duplicate test_declared_multi_install_safe (the existing
  test_declares_multi_install_safe already asserts the same thing)

* address review: keep agent-root requirement; reframe agent-context targeting

- Restore 'static, unique agent root' alongside command directory in the
  multi-install-safe definition — base.py and test_registry.py
  (test_safe_integrations_have_distinct_agent_roots) enforce both.
- Reframe the agent-context note: multi_install_safe is an integration-level
  declaration about command/skill paths, so describe context-file targeting
  as independent of it rather than calling the extension 'not multi-install
  safe'. The extension can even sync multiple anchors via context_files.

* address review: hoist multi_install_safe to top of class

Move the multi_install_safe = True declaration to the top of
KiroCliIntegration (right after key) so it is visible at the exact spot
the diff touched. The flag was never actually removed — it was declared
once further down the class — but placing it at the top makes the opt-in
unmistakable in review and keeps the single declaration. Verified the
integration still resolves multi_install_safe is True; 24 kiro-cli tests
pass.
 2026-07-23 07:41:07 -05:00
Manfred Riem
a5560fcf13 docs(scripts): document the 'py' script type and sh/ps migration plan (#3284) (#3653) 
* docs(scripts): document the 'py' script type and sh/ps migration plan (#3284)

Bring remaining docs up to date with the Python (`py`) workflow-script
variant introduced in #3277, and record the retention/deprecation plan
for the shell variants.

- AGENTS.md: document the `scripts:` frontmatter (sh/ps/py), clarify the
  `{SCRIPT}` placeholder resolution, and add a "Script Types and
  Migration" section (why py is recommended, defaults, phased sh/ps
  deprecation path). Note the Python agent-context variant.
- docs/quickstart.md, docs/local-development.md: mention the `py` variant
  and `--script sh|ps|py`.
- docs/reference/integrations.md: add `py` to the `--script` rows for
  install/switch/upgrade.
- .devcontainer/devcontainer.json: auto-approve `.specify/scripts/python/`.

Closes #3284.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
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Copilot-Session: 298d6ec2-a330-49bc-9394-fe2b77f25ff3

* docs(scripts): address review — accurate paths, prompt behavior, scoped py claims

Addresses the review on PR #3653:

- AGENTS.md: fix the agent-context Python path to its real
  `extensions/agent-context/scripts/python/` location.
- AGENTS.md: qualify that only templates that invoke a helper script
  carry `scripts:` frontmatter (constitution/specify do not).
- AGENTS.md: narrow the availability claim — `py` covers the core
  command templates; the bundled extensions ship Python scripts on disk
  but their command templates still invoke shell variants, so `--script
  py` does not yet route extension commands to Python.
- AGENTS.md / quickstart / local-development: describe the interactive
  prompt vs. non-interactive OS default instead of "auto-selects".
- local-development: add `--script py` to the wrong-script-type fix.

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* docs(scripts): trim deprecation timeline, correct parity/scope claims (review)

Addresses the second review on PR #3653:

- Remove the speculative four-phase deprecation timeline from AGENTS.md.
  A forward-looking removal schedule is roadmap content, not contributor
  guidance, and its phases lacked an actionable adoption signal. Replace
  it with the concrete contributor parity rule plus a one-line
  current-posture note pointing removal work to the #3277 epic.
- Stop stating dual-maintenance as already eliminated: reframe "single
  source of truth" as the intended direction, noting all three variants
  are still maintained in parallel today.
- Correct the parity-coverage claim: Python ports have output-parity
  tests where the contract is stdout-based and unit tests elsewhere,
  rather than every file being compared to every shell counterpart.
- Scope the `scripts:` frontmatter rule to core command templates and
  note the agent-context/git extension templates don't use it yet.

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---------

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 2026-07-22 11:46:11 -05:00
Manfred Riem
bb5a2c5424 docs(concepts): document the spec-of-specs feature breakdown approach (#3648) 
* docs(concepts): document the spec-of-specs feature breakdown approach (#3423)

Add a dedicated "Spec of Specs" concept page describing how to decompose a
large feature into a roadmap of smaller, independently-specified sub-features
using the existing Spec Kit flow. Covers the roadmap pass, the roadmap
artifact template, specifying each sub-feature, bidirectional sub-spec/roadmap
linking, keeping them in sync, a worked example, and optional automation.

Link the new page from the "Handling Complex Features" decomposition section
and add it to the docs table of contents.

Closes #3423

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* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

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 2026-07-22 09:30:17 -05:00
github-actions[bot]
b91e30a113 Add Intake Authoring Governance preset to community catalog (#3643) 
Add intake-authoring-governance preset submitted by @hindermath to:
- presets/catalog.community.json (alphabetical order)
- docs/community/presets.md community presets table

Closes #3621

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 2026-07-22 08:12:53 -05:00
Nurfitra Pujo Santiko
470ac5b6e6 feat: add Factory Droid CLI integration (#822) (#3587) 
Adds a skills-based integration for the Factory Droid CLI alongside the
existing Claude/Codex skills agents. The integration scaffolds
`.factory/skills/speckit-*` directories and documents the install step
in the devcontainer post-create script via the official npm
distribution (`npm install -g droid`), which matches the layout of every
other CLI install block above and avoids executing an unverified remote
shell installer. The integration is also added to the user-facing
supported-agent table in `docs/reference/integrations.md` so the new key
is discoverable from the published documentation, as required by the
"Updating this documentation" guideline in AGENTS.md.

Operator-supplied extra args via `SPECKIT_INTEGRATION_DROID_EXTRA_ARGS`
are appended after the canonical Spec Kit flags so the canonical flags
are always present in argv. The Factory Droid CLI parser uses
last-wins duplicate-flag semantics (verified empirically against
droid 0.175.0), so a later operator-supplied value may override the
canonical one — this is a deliberate inversion of the cursor-agent /
opencode / codex ordering.

Includes:
- `src/specify_cli/integrations/droid/__init__.py` (subpackage)
- `tests/integrations/test_integration_droid.py` (46 tests, including
  regression coverage for the no-trailing-newline frontmatter fusion
  bug, idempotent skill injection, and env-var path resolution)
- `integrations/catalog.json` entry + `updated_at` bump
- Alphabetical registration in `src/specify_cli/integrations/__init__.py`
  and `tests/integrations/test_registry.py`
- Devcontainer Droid install block via the npm distribution
  (`npm install -g droid`), replacing the earlier curl-based installer
- User-facing supported-agent table row in
  `docs/reference/integrations.md` (key `droid`, `.factory/skills/`
  layout, `/speckit-<command>` invocation)
- `AGENT_CONFIG` entry and matching alphabetical entries in
  `tests/test_agent_config_consistency.py` (`ISSUE_TEMPLATE_AGENT_KEYS`)
  and the three issue-template dropdowns (`agent_request.yml`,
  `bug_report.yml`, `feature_request.yml`) so
  `test_issue_template_agent_lists_match_runtime_integrations` keeps
  the runtime/template surfaces synchronized

Closes #822

Assisted-by: Droid (oracle-reviewer)

Assisted-by: Droid (model: MiniMax M3, autonomous)

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
 2026-07-22 07:49:48 -05:00
Ali jawwad
11ef1b35e2 docs(installation): document the 'py' (Python) script type (#3640) 
* docs(installation): document the 'py' (Python) script type

The installation guide's "Specify Script Type" section only showed
`--script sh` and `--script ps`, and the installed-variant list only
mentioned `.specify/scripts/bash/` and `.specify/scripts/powershell/`.
The CLI has a third script type, `py`: `SCRIPT_TYPE_CHOICES` in
`_agent_config.py` includes `"py": "Python"`, and `shared_infra.py`
installs a `python/` variant directory (plus the platform shell fallback)
when `--script py` is chosen.

Add the missing `--script py` force example and a `.specify/scripts/python/`
bullet so the docs match the code. Docs-only.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs(installation): frame Python as a first-class third script type

Address review feedback: update the section heading and intro so Python
is presented as a first-class script type alongside Shell and PowerShell,
matching the added --script py example and python/ variant directory.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-07-22 07:47:52 -05:00
Ali jawwad
4f4d19ba93 docs(core): document the 'py' (Python) --script type in the init option table (#3625) 
'specify init --script' accepts sh, ps, or py (init.py + SCRIPT_TYPE_CHOICES in
_agent_config.py), and 'specify init --script py' scaffolds Python scripts. The
core.md option reference listed only 'sh|ps', so a user following the canonical
docs never learns about --script py. Update the option row to sh|ps|py.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-07-22 07:34:43 -05:00
Pascal THUET
914d7b887f docs(upgrade): document integration upgrade / extension update as the project-files upgrade path (#3326) 
* docs: document manifest-aware project upgrades

Assisted-by: OpenAI Codex (model: GPT-5, autonomous)

* docs: clarify project upgrade commands

Assisted-by: OpenAI Codex (model: GPT-5, autonomous)

* docs: correct Claude skills path

Assisted-by: Codex (model: GPT-5, autonomous)
 2026-07-22 07:25:49 -05:00
github-actions[bot]
0d2e3b5e76 [preset] Add Parallel Autonomous Run Governance preset to community catalog (#3614) 
* Add Parallel Autonomous Run Governance preset to community catalog

Add parallel-autonomous-run-governance preset submitted by @hindermath to:
- presets/catalog.community.json (alphabetical order)
- docs/community/presets.md community presets table

Closes #3591

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: align preset metadata with review feedback

Assisted-by: GitHub Copilot (autonomous)

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Remove invalid preset dependency from extension requirements

Assisted-by: GitHub Copilot (model: gpt-5.6, autonomous)

---------

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 2026-07-22 06:10:50 -05:00
github-actions[bot]
01d07e2f87 [bundle] Add SicarioSpec Security & Governance Bundle to community catalog (#3636) 
* Add SicarioSpec Security & Governance Bundle to community catalog

- Adds sicario-spec v0.5.1 entry to bundles/catalog.community.json
- Adds row to docs/community/bundles.md
- Bundle provides 1 extension (sicario-guard) and 11 presets
- Required companion preset and extension catalogs are documented in README
- Validated: bundle ID, version, repository, release artifact, catalog entry shape, checklists

Closes #3619

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: revert sicario-spec bundle entry pending upstream README correction

The upstream README uses mutable raw.githubusercontent.com/main catalog URLs
instead of the v0.5.1 release-pinned URLs submitted in issue #3619, failing
the required-catalog consistency check. Removing the catalog entry and docs
row until the README is updated to match the submitted pinned URLs.

Assisted-by: GitHub Copilot (model: claude-sonnet-4-5, autonomous)

* Revert "fix: revert sicario-spec bundle entry pending upstream README correction"

This reverts commit 94ee59639f.

---------

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 2026-07-22 06:04:18 -05:00
github-actions[bot]
956ecab230 [preset] Update Autonomous Run Governance preset to v0.3.2 (#3615) 
* Update Autonomous Run Governance preset to v0.3.2

Update autonomous-run-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, description, tags, requires.extensions, updated_at)
- docs/community/presets.md community presets table

Closes #3606

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(presets): remove extension requirement from autonomous preset

Assisted-by: GitHub Copilot (model: GPT-5, autonomous)

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

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 2026-07-22 05:59:07 -05:00
github-actions[bot]
b79ae330fd [extension] Add Linear Weave extension to community catalog (#3609) 
* Add Linear Weave extension to community catalog

Add linear-weave extension submitted by @tonydwoodhouse to:
- extensions/catalog.community.json (alphabetical order)
- docs/community/extensions.md community extensions table

Closes #3603

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Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

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 2026-07-22 05:34:26 -05:00
WOLIKIMCHENG
b6b3ec49d9 docs: clarify hook priority validation semantics (#3594) 
* docs: clarify hook priority validation semantics

* docs: clarify stored hook priority normalization

---------

Co-authored-by: root <kinsonnee@gmail.com>
 2026-07-22 05:28:02 -05:00
github-actions[bot]
115bc94cce Add Intake Review Governance preset to community catalog (#3613) 
Add intake-review-governance preset submitted by @hindermath to:
- presets/catalog.community.json (alphabetical order)
- docs/community/presets.md community presets table

Closes #3604

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 2026-07-22 05:00:26 -05:00
Ben Buttigieg
5760061316 Add community bundle submission automation (#3553) 
* Add community bundle submission automation

Add the discovery-only community bundle catalog, online and offline catalog loading, and a restricted agentic workflow for validating bundle submissions and opening draft catalog PRs.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>

Copilot-Session: fbe794bc-667a-4c9e-b48b-825067debc6d

* Address community bundle review feedback

Ensure explicit install-allowed catalogs take precedence over built-in discovery, tighten component installability validation, and use issue-linked community branches.

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* Address follow-up bundle review feedback

Make offline catalog coverage content-agnostic and require autonomous catalog commits to include the assisted-by trailer.

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Copilot-Session: fbe794bc-667a-4c9e-b48b-825067debc6d

* Harden bundle catalog table rendering

Require single-line escaped Markdown table values for untrusted submission metadata. The needs-info label used by validation is now present in the repository.

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* Clear stale bundle validation labels

Allow the submission workflow to remove prior outcome labels before applying the current validation state.

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Copilot-Session: fbe794bc-667a-4c9e-b48b-825067debc6d
 2026-07-21 18:28:40 +01:00
Davide Barletta
74662cffad feat: update Bob integration to skills-based layout for Bob 2.0 (#3415) 
* feat: update Bob integration to skills-based layout for Bob 2.0

Bob 2.0 replaces the command-based workflow (.bob/commands/*.md) with
a skills-based layout (.bob/skills/speckit-<name>/SKILL.md), matching
the pattern used by Claude Code, Codex, and other skills-first agents.

- Switch BobIntegration from MarkdownIntegration to SkillsIntegration
- Update folder/dir from .bob/commands to .bob/skills
- Change extension from .md to /SKILL.md (skills layout)
- Add --skills option (default: True) consistent with Codex pattern
- Update tests to inherit from SkillsIntegrationTests (28 tests pass)
- Bump catalog entry to version 2.0.0 with updated description

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* PR comments fix: keep old Bob 1 commands till next release

* Copilot suggested change

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* feat(bob): address copilot comments, make skills layout default, demote legacy commands to opt-in

* fix(bob): honor legacy_commands in ai_skills persistence and add bob to ALWAYS_SLASH_AGENTS

- init.py: suppress ai_skills=True when --legacy-commands is passed so
  extensions and presets target .bob/commands, not .bob/skills
- _invocation_style.py: add 'bob' to ALWAYS_SLASH_AGENTS so init next-steps
  and hook invocations always show /speckit-<name> (skills is the default
  layout; no ai_skills flag required)

* Copilot suggestion

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(bob): extend IntegrationBase directly to avoid false isinstance(SkillsIntegration)

- bob/__init__.py: switch BobIntegration base from SkillsIntegration to
  IntegrationBase; add _BobSkillsHelper for skills-mode delegation; set
  invoke_separator='-' explicitly; set _skills_mode flag in setup() so
  consumers can derive the effective mode without isinstance checks
- _helpers.py: replace isinstance(integration, SkillsIntegration) guard
  with getattr(_skills_mode) so legacy-commands mode does not persist
  ai_skills=True
- _invocation_style.py: remove 'bob' from ALWAYS_SLASH_AGENTS — Bob 2.0
  skills are invoked via natural language, not /skill-name slash commands
- integrations/catalog.json: advance updated_at to 2026-07-15

* fix(lint): remove unused SkillsIntegration import from _helpers.py

* Copilot suggested change

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* feat(bob): add bob skills integration with registrar-based mode detection

* address 3 comments from copilot

* feat(bob): update registrar config to use legacy commands layout

* fix lint

* Suggested fix from Copilot

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix pr comment

* fix pr comment

* fix pr comment

* refactor(bob): resolve skills mode via base-class hooks + fix command-ref separators

Rework the dual-mode handling introduced for Bob 2.0 so an integration's
internal representation never leaks into shared init/install/upgrade code,
and fix the legacy command-reference separator surfaced in review.

Base-class contract:
- Add IntegrationBase.is_skills_mode(parsed_options) — the single hook the
  shared machinery consults to decide whether to persist ai_skills and render
  skill invocations. SkillsIntegration returns True; Copilot honors --skills /
  self._skills_mode; Bob returns `not legacy_commands`.
- Add IntegrationBase.invoke_separator_for_mode(skills_enabled) — resolves the
  command-ref separator from a project's persisted mode for registration paths
  that only have the ai_skills flag (no CLI parsed_options). Default is
  behavior-preserving; Bob maps skills->"-", legacy->".".
- BobIntegration stays on IntegrationBase (mirroring Copilot, the other
  dual-mode agent) and delegates setup() to internal _BobSkillsHelper /
  _BobMarkdownHelper. Removes the _skills_mode method and all
  isinstance(SkillsIntegration) / callable(_skills_mode) probing from
  _helpers.py and init.py.

Fix legacy separator (review feedback): CommandRegistrar.register_commands and
PresetManager._resolve_skill_command_refs previously read the single static
AGENT_CONFIGS[key]["invoke_separator"], so legacy .bob/commands/ extension and
preset command refs rendered /speckit-<cmd> instead of Bob 1.x /speckit.<cmd>.
Both now resolve the separator per project mode via invoke_separator_for_mode.

Tests: add regression coverage for the is_skills_mode / invoke_separator_for_mode
hooks and legacy extension command-ref separators; normalize a width-sensitive
workflow assertion to match its siblings. Full suite green.

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* fix(bob,copilot): address review — preserve legacy layout, dual-mode separators, extension-skill token resolution

Addresses PR review 4716036212 (3 comments):

1. Bob legacy-install regression: `use`/`switch`/`upgrade` on an existing
   Bob 1.x project (only `.bob/commands/` on disk, no stored
   `legacy_commands`) called `is_skills_mode(None)` -> True and rewrote
   `ai_skills=True`, silently switching extension/command-reference handling
   to the skills layout. `is_skills_mode` now takes an optional `project_root`;
   Bob preserves an already-installed legacy layout until an explicit upgrade
   creates `.bob/skills/`. A fresh project still defaults to skills.

2. Copilot dual-mode separator: `invoke_separator_for_mode` was inherited
   from the base (mode-independent) and returned Copilot's static `.`, so
   preset/extension command refs in a Copilot skills project rendered
   `/speckit.<name>` instead of `/speckit-<name>`. Override it on Copilot to
   track the persisted `ai_skills` state, consistent with
   `build_command_invocation` and `effective_invoke_separator`.

3. Bob extension-skill command-ref tokens: verified that merging main's
   generic `_resolve_command_ref_tokens` (#3544) resolves Bob's tokens via
   the `CONDITIONAL_SLASH_AGENTS` path (`/speckit-<name>`); added Bob to the
   command-ref regression parametrize plus dedicated Bob use-path tests.

All tests pass (full suite green; merged with current main incl. #3544).

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* fix(bob): resolve command-ref separator with project-aware mode before shared-infra refresh (review #3415)

The `use`/`switch` paths refresh shared infrastructure via
`_with_integration_setting()` / `_invoke_separator_for_integration()`,
which previously resolved the invoke separator through
`effective_invoke_separator` / `is_skills_mode` WITHOUT a project_root.
For a pre-PR Bob 1.x project (.bob/commands/ on disk, no stored options),
this defaulted to the skills "-" separator and rewrote rendered
shared-template command refs to /speckit-*, even though ai_skills stayed
false. Thread project_root through effective_invoke_separator, the two
runtime helpers, and every call site so Bob's on-disk legacy detection
governs the separator before shared infra is refreshed.

Add a rendered-shared-template regression test covering `use --force`.

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* fix(bob): scope persisted ai_skills flag to active agent when resolving command-ref separator (review #3415)

`register_commands` runs once per detected agent, but the persisted
`ai_skills` flag describes only the active integration (`opts["ai"]`).
When another agent (e.g. Copilot) is active in skills mode while a
legacy `.bob/commands` layout is also present, the previous code passed
that global `True` to Bob's `invoke_separator_for_mode`, rewriting Bob
1.x command refs to `/speckit-*` instead of `/speckit.*`.

Only consult the persisted flag for the agent it describes
(`opts["ai"] == agent_name`); otherwise resolve the separator from the
agent's own project-aware `effective_invoke_separator(None, project_root)`.

Add regression tests covering the mismatched-active-agent case and a
control for Bob-active skills mode.

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* fix(bob): detect Spec Kit layout from managed artifacts, not any skills dir (review #3415)

Two related mis-detections from review 4723246468:

1. `BobIntegration.is_skills_mode` treated the mere presence of a
   `.bob/skills/` directory as proof the project is skills-based. A legacy
   Spec Kit install (managed `.bob/commands/speckit.*.md`) that also carried
   unrelated Bob 2 skills would be misclassified as skills, so
   `integration use bob` persisted `ai_skills` and rewrote shared refs.
   Now the layout is inferred from managed Spec Kit artifacts: legacy/command
   mode only when managed `speckit.*.md` command files exist and no managed
   `speckit-*` skill dirs do.

2. The `register_commands` separator for an inactive agent used a disk-based
   `effective_invoke_separator(None, project_root)` fallback that could pick
   the skills separator even though the registrar writes the static command
   layout (`.bob/commands/*.md`). Inactive agents now resolve the separator
   from the registrar's actual output layout (`extension == "/SKILL.md"`),
   so command-layout files keep `/speckit.*` refs regardless of sibling dirs.

Update the affected hook/E2E tests to use managed artifacts and add
regression tests for the mixed-layout and inactive-registrar scenarios.

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* fix(bob): apply managed-artifact detection on upgrade + consistent skill post-processing (review #3415)

Two issues from review 4723782860:

1. `BobIntegration.setup()` resolved the layout via `is_skills_mode(parsed_options)`
   WITHOUT `project_root`, so `integration upgrade bob` on a Bob 1.x install
   (managed `.bob/commands/speckit.*.md`, no stored options) ignored the
   existing command files, generated skills, and stale-deleted the legacy
   commands — silently migrating the project. Pass `project_root` so the same
   managed-artifact detection used by `use` also governs upgrades.

2. Only `_BobSkillsHelper` overrode `post_process_skill_content` to suppress
   the shared slash-command hook note. Preset/extension skill generators call
   that hook on the registered `BobIntegration`, which inherited
   `IntegrationBase`'s note-injecting default. Repeat the no-op (delegating to
   the skills helper) on the registered class so every Bob skill-generation
   path is consistent with intent-activated core Bob skills.

Add regression tests for the upgrade-preservation and post-processing paths.

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* feat(bob): add --skills migration opt-in; fix separator + manifest loss (review #3415)

Address review #3415 (4724160183):

- Comment 1: Add an explicit `--skills` opt-in to BobIntegration. It forces
  the skills layout over on-disk auto-detection, giving legacy Bob 1.x
  installs a supported migration path
  (`integration upgrade bob --integration-options="--skills"`). `--skills`
  and `--legacy-commands` are mutually exclusive (clean exit-1 error).

- Comment 2: In CommandRegistrar.register_commands, derive the command-ref
  separator from the output layout (agent_config["extension"]) for the
  active agent too, not the persisted ai_skills flag. A command-layout file
  (.bob/commands/*.md, .github/agents/*.agent.md) always renders /speckit.*;
  only a /SKILL.md scaffold uses /speckit-*. Dual-layout agents (Bob,
  Copilot) write skills via their own setup()/skills path, so
  register_commands only ever emits their command-layout files.

- Comment 3: Update docs/reference/integrations.md Bob entry to document the
  skills-based default (.bob/skills/), the deprecated --legacy-commands
  opt-out, and the --skills migration path.

Also fix a latent manifest-loss bug surfaced by the migration path: the
upgrade Phase 2 stale-file cleanup built a throwaway manifest sharing the
integration key and called uninstall(), which always deleted
{key}.manifest.json. Any layout-shrinking upgrade (e.g. legacy->skills)
thus wiped the freshly-saved manifest, leaving the project untracked and
un-upgradeable. uninstall() now takes remove_manifest (default True); the
stale-cleanup pass passes False.

Adds regression tests for the --skills opt-in, mutual exclusion, corrected
active-agent separator, remove_manifest=False, and an end-to-end
legacy->skills migration that verifies the manifest survives and the
project remains upgradeable. Full suite: 4555 passed, 5 skipped.

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* docs(agents): align token-resolution comment with output-layout separator rule (review #3415)

Address review #3415 (4725516805). The comment above resolve_command_refs
still described the removed state-based behavior ("resolve it from the
integration using the project's persisted skills state"). Update it to
describe the output-layout rule that register_commands now uses: _sep is
derived from the layout this registrar writes (a /SKILL.md scaffold uses the
skills separator; a command-layout file uses the command separator), not the
persisted ai_skills state. Comment-only change; no behavior change.

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* fix(bob): reconcile extension artifacts on layout change (review #3415)

When a dual-mode agent (Bob) flips between the legacy commands layout and
the skills layout during `integration upgrade` (via `--skills` /
`--legacy-commands`), the old layout's extension command/skill files were
left orphaned: Phase 2 stale cleanup only removes files tracked by the
*integration* manifest, while extension artifacts are tracked in the
extension registry. Detect the layout flip by comparing whether the old vs
new manifest tracks a `/SKILL.md` scaffold, and when it changed, unregister
the agent's extension artifacts before the existing re-registration so they
are recreated in the new layout (and the per-agent registry is updated).

Preset artifacts are documented as a known, pre-existing cross-cutting gap:
no agent-scoped preset re-registration exists in use/switch/upgrade for any
agent, so reconciling them is out of scope for this Bob migration.

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* fix(bob): reject layout migration when preset overrides are installed (review #3415)

A command↔skills layout change during `integration upgrade` cannot reconcile
preset artifacts: presets track their command/skill files in per-preset
`registered_commands`/`registered_skills` metadata, and there is no
agent-scoped preset re-registration anywhere in the CLI. Migrating would
delete a preset's old-layout files without recreating them in the new layout
and leave the preset registry claiming artifacts that no longer exist.

Detect the intended layout via `is_skills_mode` (so a plain same-layout
upgrade is unaffected) and, when it flips while preset overrides are
installed for the agent, reject the upgrade *before any mutation* with an
actionable error pointing at the remove → upgrade → reinstall workaround.
Extension artifacts are still reconciled for the safe (no-preset) case.

Adds a regression test and documents the migration caveat in the Bob
integration reference entry.

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* fix(bob): restrict layout reconciliation to the active integration (review #3415)

`integration_upgrade` supports upgrading a secondary (non-active) integration,
but the layout-change extension reconciliation was unsafe there.
`ExtensionManager.unregister_agent_artifacts()` treats the unscoped
per-extension `registered_skills` list as belonging to the passed agent and,
when that agent's skills directory is absent, falls back to scanning every
agent's skills directory — so reconciling a secondary Bob layout flip could
delete or untrack the *active* agent's extension skills. The subsequent
re-registration cannot repair that because extension skill rendering is
intentionally scoped to the active agent (#2948).

Gate the unregister-before-register reconciliation on `installed_key == key`
so it only runs for the active integration. Secondary agents only ever have
extension command files (skills are active-agent-only), which the existing
re-registration rewrites in place, so skipping the unregister orphans nothing
new. Adds a regression test asserting a secondary Bob layout change leaves the
active agent's extension skill intact on disk and in the registry.

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* fix(bob): fail closed when preset registry is unreadable (review #3415)

Address review 4744636079:

- _migrate_commands: the preset guard previously failed *open* — a
  registry read/parse error returned an empty "no presets" list, so a
  --force layout-changing upgrade could delete preset-overridden command
  files while their registry state was unknown. Read the registry file
  directly and raise _PresetRegistryUnreadableError on any read/parse
  failure or malformed structure, rejecting the migration before any
  mutation. A genuinely absent registry still returns [] (safe).

- bob: correct the is_skills_mode docstring — upgrade *does* run setup();
  disk detection is needed because legacy Bob 1.x installs never persisted
  a legacy_commands option, so the stored mode is unavailable.

- tests: add fail-closed E2E (corrupted registry rejected, valid-empty
  allowed) plus a unit test for _installed_presets_affecting_agent covering
  absent / corrupted / malformed / valid / affecting-agent cases.

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* fix(bob): fail closed on malformed preset entries too (review #3415)

Address review 4745191015: the preset guard read a parseable registry but
silently skipped malformed per-preset metadata and treated a malformed
registered_commands value as "no matching artifacts". A registry such as
{"presets":{"p1":[]}} therefore allowed a layout migration even though p1's
ownership is unknown, risking deletion of preset-managed files. Now raise
_PresetRegistryUnreadableError for a non-dict preset entry, a non-dict
registered_commands, or a non-list registered_skills. Extend the unit test
to cover these malformed shapes.

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---------

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 2026-07-21 09:20:20 -05:00
github-actions[bot]
7f97f1f1f8 Update OKF Knowledge Bundle Generator to v0.3.0 (#3608) 
Update okf extension submitted by @alexcpn:
- extensions/catalog.community.json (version, download_url, description, provides.commands, updated_at)
- docs/community/extensions.md community extensions table

Closes #3602

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 2026-07-21 09:11:30 -05:00
github-actions[bot]
3b611575b2 Add Test Coverage Drift Control extension to community catalog (#3607) 
Add test-coverage-drift-control extension submitted by @benizzio to:
- extensions/catalog.community.json (alphabetical order)
- docs/community/extensions.md community extensions table

Closes #3600

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Pascal THUET
ec45dbd791 chore: align ruff lint scope (#3139) 
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