fix(core): remove os/pathlib from wiki_coverage cluster (#560, 3/3) - #569

… modules

Third and final PR of the multi-PR #560 fix: wiki_coverage.py (1330
lines, the largest of the 6 wiki-filesystem-cluster modules) had 5
functions doing real filesystem I/O (os.stat, os.listdir, os.walk,
open+read). New mcp_server/infrastructure/wiki_coverage_fs.py holds all
of it; core now goes through one configure_wiki_coverage_filesystem(
stat_page=, markdown_file_sizes=, domain_kind_membership=,
walk_source_files=, walk_markdown_contents=) injection point, wired by
mcp_server/__main__.py and tests_py/_composition_root_wiring.py (the
same idiom every other module in this multi-PR fix uses).

- _has_substantive_anchor: os.stat -> injected stat_page(wiki_root,
  rel_path) -> (size, mtime) | None.
- _count_substantive_pages: isdir+listdir+getsize -> injected
  markdown_file_sizes(dom_path) -> {filename: size}.
- list_domains: isdir+listdir membership counting across known-kind
  directories -> injected domain_kind_membership(wiki_root, known_kinds)
  -> {candidate_domain: [kind, ...]}; the plausibility filter and
  >=2-kinds threshold stay in core as pure logic over the returned dict.
- list_source_files: os.walk+splitext+relpath -> injected
  walk_source_files(root, skip_directories, source_extensions), core's
  own frozensets passed in as plain data (no I/O in the constants
  themselves).
- _index_wiki_file_references: os.walk+open+read every .md file ->
  injected walk_markdown_contents(wiki_root) returning the raw text of
  every page; the regex token-extraction stays in core (pure).
- Two bare os.path.basename() calls (pure string ops, not part of the
  walk) replaced with token.rsplit("/", 1)[-1].
- _SKIP_DIRECTORIES stopped duplicating the frozenset already extracted
  to mcp_server/shared/wiki_skip_directories.py for
  infrastructure/wiki_drift_fs.py's identical need (DRY boy-scout fix;
  that shared module exists specifically because infrastructure/ may not
  import core/, so the pure data had to move to shared/ for both infra
  modules to reuse).

Also fixes a pyright regression introduced by wiki_axis_registry.py's
fix in this same branch: configure_default_wiki_root's provider type
changed from Path | str | None to str | None (core cannot reference
Path even in a type hint without importing pathlib), so __main__.py's
own configure_default_wiki_root(lambda: WIKI_ROOT) needed to become
lambda: str(WIKI_ROOT) (WIKI_ROOT is a Path from
infrastructure/config.py) -- caught by pyright, not by any test.

Seam-fragility audit (per the #568/PR2 CI failure where a bare CI
preload script bypassed every composition root and hit an unconfigured
seam): grepped scripts/, .github/, benchmarks/, and mcp_server/hooks/
for every wiki_drift/wiki_axis_registry/wiki_coverage_dashboard/
wiki_coverage function and configure_* name introduced in this PR and
the prior wiki-cluster commit -- zero hits outside mcp_server/__main__.py,
tests_py/_composition_root_wiring.py, and handlers/. Unlike the reranker
seam, these four wiki seams have no bare-script exposure today, so their
"raise RuntimeError if unconfigured" design (correct here: a wiki audit
silently returning "no drift found" when actually misconfigured is a
worse failure mode than a loud crash, unlike an env-var read where
"unconfigured = false" is a safe default) is not a live landmine. Also
re-audited PR #564's abstention_gate.py (classifier_factory already
degrades gracefully to no-filtering when unconfigured, confirmed safe)
and codebase_graph.py (no I/O seam at all, pure string ops only).

Fixes #560 (all 17 of the audited core/ modules that imported os or
pathlib now have zero such imports; part 1/3 was PR #564, part 2/3 was
PR #568).

Verified: scripts/check_craftsmanship.py --base origin/main returns OK;
grep for os/pathlib in this branch's 6 wiki modules returns empty; ruff
check/format are clean; pyright mcp_server/ reports 0 errors; `python
scripts/verify_mcp_hosts.py -- hypermnesia-mcp` passes on all 6
client/profile combinations; full pytest in progress at commit time (see
hand-back notes for the confirmed count).

Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>

Addresses the reviewer's explicit "apply the same no-silent-default rule
to #569, for example a wiki-root seam that falls back to a default
path" note on PR #568's review.

get_registry() used to collapse "configure_default_wiki_root was never
called" and "the configured provider legitimately returned None" into
the same wiki_root=None -> defaults-only behavior. The first case is a
missing composition root, not a valid answer, and silently degrading to
built-in defaults would hide any wiki-relative custom axis taxonomy a
user configured via _schema/ files (CLAUDE.md: no silent fallbacks).
Now: an explicitly-configured provider that returns None still yields
defaults-only (unchanged, legitimate); a provider that was never
configured at all raises RuntimeError.

Wired tests_py/_composition_root_wiring.py's
configure_default_wiki_root(lambda: None) explicitly, matching the
test session's pre-existing implicit behavior (conftest.py isolates
tests from any real wiki data) but now stated rather than silently
defaulted. All 78 tests across test_wiki_axis_registry.py,
test_wiki_classifier.py, test_ble001_sweep_core.py, and
test_craftsmanship_imports.py pass unchanged.

Also fixed a malformed `source: ADR-0297, issue #560` citation in
wiki_coverage_fs.py's docstring (decision-integrity gate parses the
first token after "source:" as a single decision ID; a trailing comma
made it unparseable) -- same class of typo already fixed elsewhere in
this PR, missed on this file.

Verified: scripts/check_craftsmanship.py --base origin/main returns OK;
pyright mcp_server/ reports 0 errors; full pytest reports 8447 passed,
165 skipped, 0 failed.

Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>

…y import

CI's craftsmanship gate refused hooks/* importing the top-level
mcp_server.composition_root: the layer table lets hooks/ import core,
infrastructure and shared only. hooks/ is also the only layer that may
itself import both core and infrastructure and be imported by every
entry point (the top-level __main__, scripts and benchmarks are not
layer-checked), so the single wiring function moves to
mcp_server/hooks/wiring.py.

- post_tool_capture wires in _dispatch_with_store_cleanup, after the
  capture-mode gate, instead of inside process_event: excluded events
  still import nothing from core or infrastructure (W3-1b), and
  process_event stays within the 40-line cap.
- Single-line imports keep post_commit_reindex.py under 300 lines.
- The coverage test matches a real top-level main block, not the phrase
  quoted in a docstring.
- Measured cost of the wiring import in a hook process: 24-35 ms
  cumulative (python -X importtime, 3 runs, this machine).

Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>