chameleon 3.1.3

Second whole-plugin real-invocation QA round against the released v3.1.2,
weighted toward Python/Ruby framework depth, less-covered skills, and this
project's own newest code paths. 30 findings confirmed via independent
adversarial re-verification, resulting in 25 code and doc fixes across 15
files (several confirmed findings shared one root cause). As with the prior
round, the fix pass itself was independently re-verified per finding; that
pass caught two fix-introduced regressions (both in conventions.py, both
repaired with real two-scenario regression tests — see "Fixed").

Fixed

• A same-turn fix from the prior round crashed the SessionStart/conventions.md
  render entirely on a real Ruby repo (high). The casing-convention rendering
  added in v3.1.2 raised UnboundLocalError whenever a method/class/constant
  casing convention was "strong but not enforced" (60-95% consistency) — the
  exact tier that feature exists for — silently dropping the WHOLE conventions
  block, not just the casing line, and deleting a pre-existing
  .chameleon/conventions.md mirror outright. conventions.py.
• Trust bypass: explain_edit and get_review_history had zero trust gating
  (P1). Either tool replayed one checkout's archetype classification,
  match_quality, blockable-rule list, or PR-review verdict history — including
  free-text findings, commit SHAs, and reviewer usernames — to a caller whose
  own checkout was never granted trust for that repo_id. Both now gate on
  trust_state_for(repo_id).grants_root(repo_root) before serving content,
  mirroring every other model-callable read tool. tools.py.
• get_canonical_excerpt/get_rules could silently serve a DIFFERENT
  physical clone's content when a repo_id collided across two local
  checkouts of the same remote, with no way to detect the mismatch. The
  resolved repo_root now rides in the envelope. tools.py.
• PR-review auto-pass's override_rate was computed from shadow-mode
  would-blocks only, never real enforce-mode blocks — an actively-enforcing,
  well-behaved rule could read as a 100% override rate and get flagged
  high_override_rate with zero real sample evidence. review_ledger.py.
• get_callers/get_callees/get_blast_radius merged distinct same-named
  methods from different classes in one file into a single answer,
  contradicting the tools' own "fails open on any ambiguity" contract;
  get_blast_radius could compose a fabricated multi-hop chain from two
  unrelated methods that happened to share a name. calls_index.py.
• The multi-lens VERIFY/refuter stage refuted correct, well-evidenced
  intent-vs-code mismatch findings because it was never given the captured
  intent_tokens the correctness judge itself used to raise them — only a
  source-only excerpt, which its own prompt instructs it to refute on when it
  "cannot tell." The tokens are now folded into the refuter's copy of the
  claim for that call only, then restored before persistence/render.
  hook_helper.py.
• A real block or inline override of import-preference-violation was
  invisible to /chameleon-explain's post-incident replay — the only
  PreToolUse deny branch that never called _record_edit_decision, unlike its
  secret-detected-in-content and eval-call siblings. hook_helper.py.
• Monorepo coordinator-only bootstraps had nowhere to persist a resolved
  production_ref lock, so detect_repo silently reported locked: false
  for a workspace whose profile really was derived from a locked branch, and
  refresh_repo's inheritance fallback could silently overwrite an explicit
  lock with a freshly re-detected branch. The coordinator's resolution is now
  persisted off the trust-hashed surface and read by both paths. tools.py.
• A no-git-remote repo that lost its repo_uuid (deletion, bad merge, a
  restored old backup) silently shifted repo_id to the path-hash branch,
  orphaning the prior trust/drift/review-history grant with no diagnostic.
  detect_repo now surfaces a legacy_trust_hint, mirroring the existing
  engine-hash-change case — but declines when config.json carries a
  persisted production_ref (only ever auto-stamped for an origin-backed
  repo), since that combination means the repo more likely lost its git
  remote, not a repo_uuid it never needed; misattributing that case pointed
  at the wrong remediation (a caught-and-fixed regression in this same fix).
  tools.py.
• refresh_repo's default (force=False) path didn't detect a
  conventions.json whose derived section (e.g. naming) was stripped while
  the surrounding JSON stayed valid — reported noop and left the corruption in
  place indefinitely. tools.py.
• Pausing chameleon only silenced the auto-injected PreToolUse hook path —
  a model calling get_pattern_context directly during an active pause still
  got full guidance. The pause state is now checked inside the tool itself,
  blanking canonical/idiom/rule content with a paused reason like the
  untrusted gate does. Pausing was also invisible everywhere a user could
  check it (statusline, /chameleon-status, /chameleon-doctor) — the
  statusline now surfaces the active window. tools.py, chameleon-statusline.sh.
• doctor's hook-error log scan silently discarded the exact warning that
  signals a prose artifact (idioms.md/principles.md/conventions.md) was
  dropped for prompt injection — a live, correctly-blocked poisoning event
  left no trace in the one diagnostic tool meant to surface it. tools.py.
• get_status's enforcement.overrides block was documented as
  conditionally present but the code always included it, even with zero
  override history ever. tools.py.
• The symbol-index stale-vs-corrupt classifier treated ANY schema_version
  mismatch as "stale", including a schema_version-absent garbage payload
  bearing no resemblance to a real prior-schema artifact — now requires actual
  shape evidence before calling it stale rather than corrupt. tools.py.
• search_codebase silently reported zeroed results with no degraded flag
  when calls_index.json/symbol_signatures.json were entirely MISSING,
  even though the identical present-but-corrupt case correctly flagged
  degraded. Both now surface a reason. tools.py.
• _classify_casing's four casing buckets left a gap: a file stem mixing
  an underscore separator with an embedded uppercase letter (test_BadCasing)
  matched none of kebab/snake/camel/Pascal and returned no signal, so the
  file-naming-violation rule silently never fired on exactly the shape that
  most obviously breaks a repo's casing convention. Added a mixed_case
  bucket that counts against consistency — and, caught by this same round's
  independent review, a follow-up fix so mixed_case can never itself win the
  dominance vote and become the archetype's own declared "convention" (which
  would have flagged every genuinely-conforming sibling as a violator).
  conventions.py.
• The Python naming-convention lint check was ASCII-only, misclassifying
  every legal PEP-3131 unicode identifier as a casing violation even when
  genuinely conforming in its own script — on a BLOCK_ELIGIBLE rule, capable
  of hard-blocking a correct edit. Casing classification is now based on
  actual letter case (str.isupper()/isupper() semantics), not an
  ASCII character-range regex. conventions.py.
• A multi-base Python class's extends display marker ("Base (+1 more)")
  was reused as a dominance-grouping key, fragmenting a shared primary base
  across single- and multi-base classes into separate Counter buckets and
  potentially defeating a real, unanimous base-class contract — caught by this
  round's independent review of the libcst_dump.py fix that introduced the
  marker. Dominance grouping now uses the plain first base; the display marker
  is TS/Python-render-only. conventions.py.
• The journey harness's "no concurrent runner" lock could never actually
  detect a concurrent invocation — build_context() created the exclusive,
  uniquely-timestamped run_dir one call before the lock was ever acquired, so
  two overlapping invocations just created two different run_dirs and never
  contended; a real race crashed with an unhandled FileExistsError instead of
  the documented clean PreflightError. The lock now scopes to (and is
  acquired against) the shared results root BEFORE any run_dir is created.
  preflight.py, runner.py.
• The new slash-path intent-capture regex required a leading /, silently
  truncating the far more common relative repo-path form a user actually types
  (src/config/settings.ts) instead of capturing it whole. The new
  single-digit numeral rules didn't exclude a following /, so a fraction
  or ratio (retries=1/3) captured its numerator as a standalone checkable
  constant. intent_capture.py.
• chameleon-teach/SKILL.md documented zero working examples of the
  Source: provenance line for either capture mode, despite the doc's own
  cap description, validation-error table, and Honesty Rules section assuming
  it was in use. chameleon-deep-work/SKILL.md's dependency-baseline step
  assumed a lockfile always exists, with no guidance for a lockfile-less
  repo. Both docs updated.
• tests/bench_hot_path.py's target-file selection ignored the profiled
  repo's own declared language, always preferring .tsx/.ts over .rb,
  so a Ruby repo with any frontend TypeScript file silently benched an
  unmatched-archetype degraded path instead of the intended Ruby hot path.

Full unit suite green (5634 passed, 3 skipped), ruff clean.