* fix(continuous-learning): cluster instincts by keyword overlap in /evolve
`cmd_evolve` grouped instincts by exact string equality of the whole
normalized trigger sentence. Triggers are free-form sentences, so every
instinct landed in its own bucket and `skill_candidates` was always empty.
`agent_candidates` is derived from `skill_candidates`, so agents never
generated either — `/evolve --generate` could only ever emit commands.
Measured on a 42-instinct project: 42 instincts produced 42 unique cluster
keys, largest cluster size 1.
Group on keyword overlap instead. Jaccard is the wrong metric here — trigger
keyword sets average ~7 words, so even clearly related pairs top out around
0.33 — so this uses the overlap coefficient (shared / smaller set) at 0.5,
plus a floor of 2 shared keywords so one incidental word cannot pull
unrelated instincts together. The same 42 instincts now yield 4 clusters.
Also unify the command/agent slug used by the preview and the writer. The
preview called `.replace('a ', '')`, which strips "a " anywhere in the
string, mangling "extracting data from Reddit" into
`/extracting-datfrom-R` while `--generate` wrote `extracting-data-from.md`.
Both paths now share `_evolved_command_name()` / `_evolved_agent_name()`.
Adds tests/scripts/instinct-cli-evolve.test.js, which fails on the previous
implementation (0 clusters instead of 1; preview name `extracting-datfrom-R`)
and covers the negative cases so unrelated triggers still stay apart.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
* docs(continuous-learning): correct clustering metric name in docstring
The docstring said "Jaccard" while the implementation uses the overlap
coefficient, which is the point of the change.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
* fix(continuous-learning): generate every evolve candidate and cut slugs on word boundaries
_generate_evolved() wrote only skill_candidates[:5], workflow_instincts[:5]
and agent_candidates[:3]. On a project with 36 command candidates that meant
5 files and no warning, so the output read as complete while 86% of the
candidates were dropped.
Generation is now unbounded by default and takes a --limit N flag for callers
that want a cap. A cap that truncates says so:
Note: writing 3 of 36 command candidates (--limit 3); 33 skipped.
The analysis preview keeps showing five per kind but now names the remainder
("... and 31 more command candidates not shown") instead of presenting a
sample as the whole set.
Slugs were also cut with a hard slice, which split words mid-token and
produced /investigating-comple, /learning-about-compl and
/researching-mechanis. _truncate_slug() retreats to the last separator that
fits, and keeps the full head when the cut already lands on one, so
"analyzing large text files" stays /analyzing-large-text rather than losing
a word. A first word longer than the limit still falls back to a hard cut
because no boundary is available.
Shorter slugs collide more easily, and a collision used to mean one file
silently overwriting another. _assign_unique_slugs() suffixes duplicates
(-2, -3) and is called by both the preview and the writer over the same
ordered list, so advertised names and written names cannot drift apart.
Skill directory naming moved to _evolved_skill_name(); it previously used its
own inline slug expression, so it was the one truncation the shared helper
did not cover.
Adds tests/scripts/instinct-cli-evolve-generate.test.js: 7 cases covering
word-boundary cuts, the separator-aligned cut, unbounded generation, --limit
reporting, collision dedup, preview remainder and preview/writer agreement.
Six of the seven fail against the previous implementation.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
Co-authored-by: haelyra <49814733+haelyra@users.noreply.github.com>
Honor an explicit non-git CLAUDE_PROJECT_DIR as an isolated project scope, canonicalize and hash it consistently in the shell observer and Python CLI, and preserve the global fallback for arbitrary non-git working directories.
* fix(clv2): align Python _update_registry schema with shell counterpart
The Python `_update_registry` in instinct-cli.py wrote registry entries
without the `id` and `created_at` fields, while the shell counterpart in
detect-project.sh writes both. A projects.json entry could therefore have a
different shape depending on which path (Python CLI or shell hook) last
touched it.
Emit the same field set and order as the shell version: id, name, root,
remote, created_at (preserved from any existing entry), last_seen. Add
regression tests asserting field parity and created_at preservation.
Fixes#2299
* fix(clv2): guard _update_registry against a non-dict registry entry
A malformed projects.json (a non-dict value for the current project id, e.g.
null) would make existing.get("created_at", ...) raise and crash the update,
losing the old code's ability to self-heal a corrupt per-entry value. Normalize
existing to {} when it is not a dict so the entry is healed by the rewrite. Add
a regression test for the malformed-entry path.
* test(clv2): assert the first-write created_at == last_seen contract
The new _update_registry tests only checked both timestamps were truthy. On the
initial write both derive from the same `now`, so created_at must equal
last_seen; assert that explicitly so a later refactor that breaks the contract
is caught. Split the compound assertions into single-expression checks.
* fix(clv2): heal a non-dict top-level registry in _update_registry
A projects.json that is valid JSON but not a mapping (e.g. `[]` or a
string) previously crashed _update_registry on registry.get(), before
the per-entry guard could run, so the corrupt file could not be healed.
Guard the top-level shape right after the load and fall back to {} so the
rewrite repairs the file — matching the per-entry healing already in place.
Resolves the remaining CodeRabbit finding on #2299.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Two security-priority fixes in continuous-learning-v2/scripts/instinct-cli.py:
- #2294: _write_registry wrote projects.json without the advisory lock that
_update_registry holds, so concurrent 'projects delete/gc/merge' could race an
observe-time update and corrupt the registry. Extract the lock into a shared
_registry_lock() context manager and use it in both writers.
- #2297: _remove_project_storage called shutil.rmtree on PROJECTS_DIR/project_id
with no containment check. Add defense-in-depth: resolve the path and refuse to
delete anything that is not strictly inside PROJECTS_DIR (or is the root
itself), so a relaxed validator or future caller can never cause an
arbitrary-directory delete.
Adds 5 pytest regression tests (atomic write under lock, contained delete,
missing-dir no-op, traversal refused, root refused). Node integration suite
(tests/scripts/instinct-cli-projects.test.js) green 9/9.
* fix: surface legacy data warning in instinct-cli status (#2036)
When the data directory moved from ~/.claude/homunculus/ to the
XDG-compliant ~/.local/share/ecc-homunculus/, legacy installs with data
still in the old path saw "No instincts found" with no explanation.
Add _warn_legacy_data() to cmd_status so users get a clear, actionable
warning pointing them to the migration script or the CLV2_HOMUNCULUS_DIR
override. Wrap the directory scan in try/except to handle permission
errors gracefully.
Closes#2036
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
* fix: address review feedback — drop unused f-strings, resolve absolute migrate path
Remove extraneous f-prefix from strings without interpolation (ruff F541).
Resolve migrate-homunculus.sh path relative to instinct-cli.py instead of
hard-coding a repo-relative path that only works from the repo root.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
* fix: quote migrate script path to handle spaces
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
---------
Co-authored-by: kky <lingmu141592@gmail.com>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
* feat: add pending instinct TTL pruning and /prune command
Pending instincts generated by the observer accumulate indefinitely
with no cleanup mechanism. This adds lifecycle management:
- `instinct-cli.py prune` — delete pending instincts older than 30 days
(configurable via --max-age). Supports --dry-run and --quiet flags.
- Enhanced `status` command — shows pending count, warns at 5+,
highlights instincts expiring within 7 days.
- `observer-loop.sh` — runs prune before each analysis cycle.
- `/prune` slash command — user-facing command for manual pruning.
Design rationale: council consensus (4/4) rejected auto-promote in
favor of TTL-based garbage collection. Frequency of observation does
not establish correctness. Unreviewed pending instincts auto-delete
after 30 days; if the pattern is real, the observer will regenerate it.
Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)
Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>
* fix: remove duplicate functions, broaden extension filter, fix prune output
- Remove duplicate _collect_pending_dirs and _parse_created_date defs
- Use ALLOWED_INSTINCT_EXTENSIONS (.md/.yaml/.yml) instead of .md-only
- Track actually-deleted items separately from expired for accurate output
- Update README.md and AGENTS.md command counts: 59 → 60
Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)
Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>
* fix: address Copilot and CodeRabbit review findings
- Use is_dir() instead of exists() for pending path checks
- Change > to >= for --max-age boundary (--max-age 0 now prunes all)
- Use CLV2_PYTHON_CMD env var in observer-loop.sh prune call
- Remove unused source_dupes variable
- Remove extraneous f-string prefix on static string
Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)
Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>
* fix: update AGENTS.md project structure command count 59 → 60
Co-Authored-By: Claude <noreply@anthropic.com>
* fix: address cubic and coderabbit review findings
- Fix status early return skipping pending instinct warnings (cubic #1)
- Exclude already-expired items from expiring-soon filter (cubic #2)
- Warn on unparseable pending instinct age instead of silent skip (cubic #4)
- Log prune failures to observer.log instead of silencing (cubic #5)
Co-Authored-By: Claude <noreply@anthropic.com>
* fix: YAML single-quote unescaping, f-string cleanup, add /prune to README
- Fix single-quoted YAML unescaping: use '' doubling (YAML spec) not
backslash escaping which only applies to double-quoted strings (greptile P1)
- Remove extraneous f-string prefix on static string (coderabbit)
- Add /prune to README command catalog and file tree (cubic)
Co-Authored-By: Claude <noreply@anthropic.com>
---------
Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Happy <yesreply@happy.engineering>
The observer agent creates instinct files as .md with YAML frontmatter,
but load_all_instincts() only globbed *.yaml and *.yml. Add *.md to the
glob so instinct-cli status discovers all instinct files.
- Load both .yaml and .yml files in load_all_instincts() (#216)
The *.yaml-only glob missed .yml files, causing 'No instincts found'
- Implement evolve --generate to create skill/command/agent files (#217)
Previously printed a stub message. Now generates SKILL.md, command .md,
and agent .md files from the clustering analysis into ~/.claude/homunculus/evolved/
parse_instinct_file() was appending the instinct and resetting state
when frontmatter ended (second ---), before any content lines could be
collected. This caused all content (Action, Evidence, Examples) to be
lost during import.
Fix: only set in_frontmatter=False when frontmatter ends. The existing
logic at the start of next frontmatter (or EOF) correctly appends the
instinct with its collected content.
Fixes#148
