10 Commits

Author	SHA1	Message	Date
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
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
Quratulain-bilal	d9e4565cf8	fix(integrations): escape Rich markup in --integration-options error messages (#3458) ... * fix(integrations): exit cleanly on malformed --integration-options quoting _parse_integration_options called shlex.split(raw_options) unguarded. an unbalanced quote (e.g. --integration-options='--commands-dir "foo') makes shlex raise ValueError('No closing quotation'), so a raw traceback escaped instead of the typer.Exit(1) error every other bad-input path in this function produces. reachable from specify init and every integration install/switch/ upgrade/migrate that accepts --integration-options. wrap the split and convert ValueError into the same clean CLI error. added a regression test; confirmed it fails on the pre-fix code (raw ValueError). * escape user-controlled values in integration-options error messages the malformed-quoting handler (and the unexpected/unknown option branches) interpolate raw_options/token into console.print. a value carrying an unbalanced rich tag like '--commands-dir "[/red]foo' first trips the intended shlex ValueError, but the error print then raises rich.errors.MarkupError and leaks a traceback anyway. escape all three before printing so the clean typer.Exit survives. added a regression covering both the shlex path and a bare markup token. * address review: drop redundant, mis-described markup test The removed test's docstring claimed the shlex failure branch interpolates raw_options into console.print; it only prints {exc}, which never contains the caller's markup. Its two assertions also duplicated test_bad_option_token_with_rich_markup_exits_cleanly (the '[/red]foo' case) and the shlex-path case already covered by test_unbalanced_quote_exits_cleanly. The real change here remains the escape() of the two user-controlled token prints.	2026-07-22 06:50:45 -05:00
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 Assisted-by: IBM Bob (model: claude-sonnet-4-5, autonomous) * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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). Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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`. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf * 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. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com> Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com> Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>	2026-07-21 09:20:20 -05:00
Manfred Riem	2fb18c73cb	fix(integration): preserve ai_skills on use for skills-mode Copilot (#3550) (#3551) ... `specify integration use copilot` against a Copilot install configured with `--integration-options "--skills"` dropped `"ai_skills": true` from init-options.json and regenerated extension commands in the legacy `.agent.md`/`.prompt.md` layout, contradicting `integration.json`'s stored `parsed_options.skills: true`. `_update_init_options_for_integration` only inspected `SkillsIntegration` / the instance `_skills_mode` flag. On the `use` path no `setup()` runs, so the freshly-resolved Copilot instance has `_skills_mode == False` and the stored skills intent in `parsed_options` was ignored. Thread the resolved `parsed_options` through and treat `parsed_options["skills"]` as skills mode. Adds a regression test that resets the registry singleton's `_skills_mode` to simulate a fresh process (in-process singleton reuse otherwise masks the bug). Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Copilot-Session: 06fb6ae9-f444-4dfd-ab3f-d0669c5d0604 Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>	2026-07-15 11:18:54 -05:00
Noor ul ain	c05a626cbc	fix(integrations): exit cleanly on unbalanced quote in --integration-options (#3457) (#3466) ... * fix(integrations): exit cleanly on unbalanced quote in --integration-options (#3457) `_parse_integration_options` called `shlex.split(raw_options)` unguarded, so an unbalanced quote in the flag value (e.g. `--integration-options='--commands-dir "foo'`) made shlex raise `ValueError: No closing quotation` and a raw traceback escaped — unlike every other bad-input path in this function (unknown option, missing value, unexpected value), which print a message and exit 1. Reachable from `specify init --integration-options=...` and every `specify integration install/switch/upgrade/migrate --integration-options=...`. Wrap the split in a try/except ValueError that prints a one-line error and raises `typer.Exit(1)`, matching the existing loud-fail UX. Add a test asserting the unbalanced-quote input raises `typer.Exit` with exit code 1. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>	2026-07-13 14:33:02 -05:00
Manfred Riem	53d9543355	feat: make agent-context extension a full opt-in (#3097) ... * docs: add Spec Kit spec for agent-context full opt-in Use Spec Kit's own specify workflow to author the spec that makes the agent-context extension a full opt-in, removing all agent-context configuration/support from the Python codebase and removing the deprecation message. Force-added despite specs/ being gitignored; the generated artifact will be purged prior to merge. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: add Spec Kit plan artifacts for agent-context full opt-in Phase 0/1 of the SDD plan workflow: plan.md, research.md, data-model.md, quickstart.md, and contracts/cli-behavior.md. Constitution Check is a documented no-op (repo has no ratified constitution). Force-added despite specs/ being gitignored; generated artifacts will be purged prior to merge. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: correct Constitution Check against ratified v1.0.0 Earlier draft wrongly treated the gate as a no-op; the fork's main is 16 commits behind upstream/main, which carries .specify/memory/constitution.md. Re-evaluate the feature against Principles I-V (all PASS) and note that Principle I mandates keeping context_file as a declared class attribute, validating the R1 metadata decision. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: refresh plan artifacts against synced upstream/main After syncing fork main to upstream and rebasing, re-scan the current agent-context surface. Upstream generalized the single context_file into a plural context_files concept with new resolver helpers (_resolve_context_files, _resolve_context_file_values, _format_context_file_values) and upsert/remove now loop over multiple files. Update research.md, data-model.md, contracts, quickstart grep guards, and the plan summary to cover the expanded removal scope. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: add Spec Kit tasks for agent-context full opt-in Phase 2 of SDD: dependency-ordered tasks.md (30 tasks) organized by the three user stories, with mandatory test tasks (Constitution Principle II) and a foundational phase decoupling __CONTEXT_FILE__ resolution from the extension config. Includes the extension self-seeding task (T015) and a static guard test (T002) enforcing zero agent-context references in the CLI. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * feat!: remove agent-context lifecycle from the Specify CLI Make the agent-context extension a full opt-in. The CLI no longer installs the extension during init, writes agent-context-config.yml, or creates/updates/removes the managed Spec Kit section in agent context files. Context-section upsert/remove, marker resolution, extension-enabled gating, the config helpers, and the obsolete inline deprecation warning are all removed. Integration context_file stays as inert metadata; __CONTEXT_FILE__ now resolves from registry metadata. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * feat(agent-context): self-seed context file from the active integration When agent-context-config.yml has no context_file/context_files, the bundled bash and PowerShell update scripts now resolve the context file from the active integration in .specify/init-options.json via the integration registry, so the extension no longer depends on the CLI writing its config. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * test+docs: update suite and docs for agent-context opt-in Update integration/extension tests to expect no agent-context install, config, or context-section writes during init. Add a static guard test (test_agent_context_cli_free.py) asserting the CLI source is free of agent-context lifecycle symbols, plus backward-compatibility tests for legacy projects. Refresh AGENTS.md, the extension README, and add a CHANGELOG entry describing the opt-in behavior change. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix(agent-context): warn on self-seed failure, correct docs, speed up guard test Address PR review feedback: - Self-seed scripts (bash + PowerShell) now emit an actionable warning when an active integration is configured but specify_cli cannot be imported by the chosen Python (e.g. pipx installs), or when the integration declares no context file, instead of silently falling through to 'nothing to do'. - Correct the extension README disable note: command rendering never reads the extension config; __CONTEXT_FILE__ is always substituted from integration metadata, so a stale context_files value cannot affect rendering. - Cache CLI source reads in the static guard test via a module-scoped fixture so the directory walk happens once instead of once per forbidden symbol. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * feat(agent-context): ship self-owned per-agent context-file defaults The extension now bundles agent-context-defaults.json (key→context_file map) and self-seeds from it, dropping any dependency on the Specify CLI registry. Both the bash and PowerShell update scripts read the bundled JSON map keyed by the active integration from init-options.json. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * feat!: remove all agent-context state from the Specify CLI Strip every context_file reference from the CLI: the field on all 35 integration classes, the IntegrationBase plumbing (process_template param/step, _context_file_display, docstrings), the __CONTEXT_FILE__ resolution in agents.py, the legacy context_file/context_markers popping in _helpers.py, and the context_file template in integration_scaffold.py. Also drop the Agent context update step and __CONTEXT_FILE__ placeholder from templates/commands/plan.md. The agent-context extension now solely owns all context-file knowledge, including the per-agent default mapping. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * test: drop context_file coverage and guard against CLI reintroduction Remove CONTEXT_FILE attrs and context_file assertions across the base mixins, all 35 per-integration test files, shared integration tests, and conftest stubs. Rewrite the base-mixin context tests to assert no managed section is written and no __CONTEXT_FILE__ placeholder survives. Extend the CLI-free static guard to forbid context_file, __CONTEXT_FILE__, and _context_file_display in src/specify_cli, and have the extension tests copy the bundled defaults JSON so self-seed runs without the CLI. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: reflect full removal of agent-context state from the CLI Update AGENTS.md (integration examples, required-fields table, context behavior section, pitfalls), CHANGELOG, and the SDD spec artifacts (FR-007, SC-002, data-model) to state that the CLI carries no context_file and the extension fully owns the per-agent default mapping via agent-context-defaults.json. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: align SDD artifacts with full context_file removal Update research.md (R1, R2, R4, summary table), contracts/cli-behavior.md (C3, C5), tasks.md (Phase 2, T026, notes), plan.md (Principle I, source map), and checklists/requirements.md so the spec artifacts reflect the implemented decision: the CLI carries no context_file attribute or __CONTEXT_FILE__ resolution, and the per-agent defaults map lives in the extension. Resolves PR review #4548130110. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: scrub stale context-file mentions from CLI docstrings Update the multi_install_safe docstring (drop the removed "context file" invariant), the RovoDev setup docstring (no longer upserts a context section), the Copilot module docstring (drop the context-file line), and tighten the _update_init_options_for_integration note. Pure docstring changes — no behavioral impact. Resolves PR review #4548237085. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * test+docs: harden agent-context test helper and fix stale docs - base.py: document multi_install_safe as an optional subclass attribute in the IntegrationBase docstring. - test_cli.py: clarify the init-options assertion is guarding against leftover legacy agent-context keys, not relocation. - test_extension_agent_context.py: _install_agent_context_config now asserts the bundled agent-context-defaults.json exists and always copies it, so self-seeding tests fail loudly instead of silently skipping when the map is missing. - test_integration_cursor_agent.py: drop Path/IntegrationManifest imports left unused after removing the context-section frontmatter tests. Resolves PR review #4548293116. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * chore: remove gitignored SDD artifacts from specs/ The specs/001-agent-context-full-optin/ artifacts were force-added for dogfooding visibility, but specs/ is gitignored and these were always intended to be purged before merge. Remove them so merging does not add an intentionally-untracked directory to repo history. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * chore: keep CHANGELOG.md identical to upstream CHANGELOG.md is auto-generated at release time, so the branch should not carry a manual entry. Restore it to match upstream/main exactly. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix: preserve Cursor .mdc frontmatter in agent-context updater scripts The bundled agent-context updater scripts wrote the managed section as plain text. For Cursor-style `.mdc` targets this dropped the required `---\nalwaysApply: true\n---` frontmatter, reintroducing the rule-loading bug originally fixed in #1699. Port the `_ensure_mdc_frontmatter` logic into both the bash and PowerShell updaters: prepend frontmatter when missing, repair `alwaysApply` when set to the wrong value, and leave non-`.mdc` targets untouched. Add regression tests covering both shells. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * test: scope CLI-free guard to agent-context-specific symbols Drop the bare "context_file" substring from FORBIDDEN_SYMBOLS so the guard no longer fails on unrelated future CLI fields named context_file. The list still covers agent-context-specific identifiers (__CONTEXT_FILE__, _context_file_display, _resolve_context_files, _resolve_context_file_values). Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix: harden agent-context bash self-seed against malformed init JSON Two robustness fixes in the embedded Python self-seed logic: - Coerce the integration value from init-options.json to a string only when it is actually a string; otherwise treat it as unset so a corrupted dict/list value degrades to the existing nothing-to-do behavior instead of breaking the agents-map lookup. - Normalize agent-context-defaults.json: only use 'agents' when both the JSON root and the 'agents' value are dicts, so a wrong-shaped (but valid) JSON falls back to the warning path instead of raising on .get. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix: correct PowerShell hyphenated key lookup and regex replace count - Self-seed now reads the defaults mapping via $defaults.agents.PSObject.Properties[$integrationKey].Value instead of member access ($defaults.agents.$integrationKey), which parsed hyphenated keys like 'cursor-agent'/'kiro-cli' as subtraction and failed to resolve. - Replace the static [regex]::Replace(..., 1) call, whose trailing 1 was interpreted as RegexOptions.IgnoreCase rather than a replacement count, with an instance Regex whose Replace(input, replacement, 1) limits to the first match as intended. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix: make bash .mdc frontmatter guard case-insensitive The bash updater only injected Cursor .mdc frontmatter when ctx_path ended in lowercase '.mdc', so a mixed/upper-case extension (e.g. specify-rules.MDC) was skipped and Cursor would not auto-load the rule file. Compare against the casefolded path. The PowerShell variant already uses -match, which is case-insensitive by default, so no change is needed there. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: document separator-agnostic agent-context update invocation The README hard-coded the dot-notation slash command (/speckit.agent-context.update), which hyphen-separator agents like Forge and Cline do not recognize. Document the canonical command ID plus both slash invocations so users copy the form their agent accepts. Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-06-29 15:27:26 -05:00
Pascal THUET	ce01877610	fix: register enabled extensions for agent on integration use/upgrade (#2949) ... * fix: register enabled extensions for agent on integration install/upgrade install and upgrade only set up the integration's own core commands; only switch re-registered the enabled extensions' commands for the target agent. A second integration added via install (or refreshed via upgrade) was therefore silently missing the extension commands the existing agents already had (e.g. the bundled agent-context extension). Extract switch's registration into a shared _register_extensions_for_agent helper and call it from install and upgrade too, so every installed agent ends up with every enabled extension's commands — full parity with switch. Closes #2886 * test: pin skills-mode secondary-agent registration; document #2948 limitation Extension skill rendering is scoped to the active agent (init-options track a single ai / ai_skills pair), so a skills-mode agent registered while not active (e.g. Copilot --skills installed as a secondary integration) gets command files rather than skills. install/upgrade match extension add here; only switch renders skills, because it activates the target first. Add a regression test pinning this behavior and document the limitation on the shared helper. Per-agent skills parity is tracked separately in #2948. * fix: don't re-render the active agent's skills when registering a non-active agent register_enabled_extensions_for_agent runs an active-agent-scoped skills pass (_register_extension_skills resolves the skills dir from init-options["ai"], ignoring the passed agent). Routing install/upgrade of a secondary integration through it re-rendered the *active* skills-mode agent's extension skills as a side effect — resurrecting skill files the user had deliberately deleted. Gate the skills pass on the target being the active agent; switch is unaffected because it activates the target first. Also harden the skills-mode install test (assert a core skill so --skills is load-bearing, drop a vacuous registered_skills assertion) and add a regression test. Surfaced by review of the PR; skills parity for non-active agents stays tracked in #2948. * refactor: share the extension-op scaffold and run (un)registration post-commit Review cleanups, no behavior change on the success path: - Extract the best-effort ExtensionManager scaffold (lazy import, instantiate, except -> _print_cli_warning) into _best_effort_extension_op. Both _register_extensions_for_agent and a new _unregister_extensions_for_agent delegate to it, removing the duplicate block left inline in switch. - Invoke the best-effort extension registration AFTER the install/switch/upgrade try/except has committed, so a failure in it can never trigger the rollback (install and switch teardown on except). * docs: clarify extension registration parity scope * fix(integrations): defer extension registration until use * fix(tests): remove redundant shutil import * fix(integrations): backfill extensions for installed switch targets	2026-06-22 17:48:55 -05:00
Austin Z.	bbdf1b8f40	fix(agent-context): support multiple context files safely (#2969) ... * fix(agent-context): support multiple context files safely * fix(agent-context): harden context file validation * fix(agent-context): preserve disabled context target * fix(agent-context): address review follow-ups * fix(agent-context): dedupe PowerShell context files * fix(agent-context): align context file dedupe * fix(agent-context): align bash context file dedupe * fix(agent-context): preserve disabled display target * fix(agent-context): require yaml-capable updater python * fix(agent-context): preserve context files config * fix(agent-context): align context file fallbacks * fix(agent-context): share context file resolution --------- Co-authored-by: AustinZ21 <AustinZ21@users.noreply.github.com>	2026-06-22 12:10:55 -05:00
darion-yaphet	ee17b04784	refactor(integrations): co-locate integration commands in integrations/ domain dir (PR-5/8) (#2720) ... * refactor(integrations): co-locate integration commands in integrations/ domain dir - Remove commands/ stubs (handlers will live in domain dirs) - Move all integration CLI handlers out of __init__.py into integrations/ - Split into focused modules under integrations/: _helpers.py (340 lines) — domain helpers _install_commands.py (306 lines) — install / uninstall _migrate_commands.py (487 lines) — switch / upgrade _query_commands.py (442 lines) — list / use / search / info / catalog _commands.py (34 lines) — app objects + register() - __init__.py reduced by ~1400 lines; integration block replaced with register() call - Fix patch paths in tests to new module locations * fix(integrations): restore original integration list output in refactor Preserve the CLI Required column, post-table default/installed summary, and no-installed guidance that were dropped during the no-behavior-change refactor of integration list into _query_commands.py. * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * fix(integrations): restore _clear/_update_init_options public imports The refactor that split integration commands moved _clear_init_options_for_integration and _update_init_options_for_integration into integrations/_helpers.py, but tests still import them from the top-level specify_cli package, causing ImportError. Re-export them with explicit aliases at the end of __init__.py to preserve the public import surface. --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>	2026-06-02 12:21:19 -05:00