fix(core): remove pathlib from abstention_gate and codebase_graph (#560, 1/3) - #564

… 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]>

…569)

* wip(core): remove os/pathlib from wiki_groomer/file_doc_skeleton/drift/axis_registry/coverage_dashboard (#560)

Checkpoint commit, not yet pushed: 5 of the wiki-cluster's 6 modules done
(wiki_coverage.py remains). Same injection-seam idiom as the ablation/
env-flag PR (#568), but this checkpoint has NOT yet been audited for the
"unconfigured raises" ordering-contract problem the orchestrator flagged
on that PR — every provider here needs the same audit before this is
pushed for review.

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

* fix(core): remove os/pathlib from wiki_coverage.py, last of #560's 17 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]>

* fix(core): wiki_axis_registry get_registry raises on an unwired seam

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]>

* fix(core): one composition root wires every #560 seam at every entry point

Review of #569 found the wiki filesystem seams wired only in __main__ and
the test conftest while they raise when unwired: the SessionStart-spawned
hooks/consolidate_background.py runs consolidate with wiki=True in its own
process, so every autonomous consolidation lost its dashboards (the
sub-task error was recorded nested in stats and the cycle still reported
status=ok). scripts/regenerate_file_docs.py had the same gap.

- mcp_server/composition_root.py: wire_composition_root(), idempotent,
  wires the wiki root, the schema reader and the coverage, drift and
  dashboard filesystems in one place.
- Called by __main__, scripts/launcher.py, every hooks/*.py __main__
  block, every script and benchmark runner that reaches core.
- tests_py/scripts/test_composition_root_wiring_coverage.py enumerates
  the entry points mechanically (plugin.json hook commands, hooks with a
  __main__ block, scripts and benchmarks importing core/handlers) and
  requires an actual wire_composition_root() call in each.
- tests_py/hooks/test_consolidate_background_wiki_composition_root.py
  runs the hook as a real subprocess on a throwaway SQLite store without
  the test conftest. Measured: unwired, the hook logs
  "dashboards=error: RuntimeError: ... not configured"; wired, it logs
  "dashboards=written=0". The hook's wiki summary line now reports the
  dashboard outcome instead of defaulting to "ok".

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

* fix(core): wiring lives in hooks/, the one layer every entry point may 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]>

---------

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

…g modules (#560, 3/3)

Last of the three #560 PRs (after #564 and #569): ablation.py,
conflict_monitor.py, pg_recall_weights.py, recall_pipeline.py,
reconsolidation.py, reranker_model.py, retrieval_dispatch.py,
telemetry.py and thermodynamics.py no longer import os or pathlib.

- core/environment.py: read_environment_variable/read_environment_float
  read through an injected reader, evaluated on every call, so runtime
  toggles (CORTEX_ABLATE_*, CORTEX_DECAY_DISABLED, CORTEX_*_BETA) still
  take effect after import. An unconfigured reader raises: returning
  "unset" silently would make every ablation run measure the un-ablated
  system (benchmarks set CORTEX_ABLATE_* without importing __main__).
- core/reranker_model.py: the FlashRank cache lookup, existence check and
  sha256 move to infrastructure/reranker_cache.py behind a seam that
  raises when unwired.
- Both seams join the wiki seams in mcp_server.hooks.wiring
  .wire_composition_root(), the single function every entry point calls.
  It now re-applies its bindings on every call instead of short-circuiting
  after the first, so a seam reset by a test is restored. The per-hook
  copies, benchmarks/lib/_environment_wiring.py, _reranker_wiring.py and
  the import-time wiring in hooks/_telemetry.py are gone;
  benchmarks/lib/_composition_root_wiring.py calls the same function.
- doctor.ensure_reranker_ready() wires through that function; CI's
  reranker preload step calls it instead of reaching into core directly.
- tests_py/benchmarks/test_ablation_runner_wiring.py drives the
  ablation-runner path with a CORTEX_ABLATE_* flag and proves the
  mechanism is disabled.

Fixes #560

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

…g modules (#560, 2/3) (#568)

* fix(core): remove os/pathlib from ablation.py and 8 retrieval env-flag modules (#560, 3/3)

Last of the three #560 PRs (after #564 and #569): ablation.py,
conflict_monitor.py, pg_recall_weights.py, recall_pipeline.py,
reconsolidation.py, reranker_model.py, retrieval_dispatch.py,
telemetry.py and thermodynamics.py no longer import os or pathlib.

- core/environment.py: read_environment_variable/read_environment_float
  read through an injected reader, evaluated on every call, so runtime
  toggles (CORTEX_ABLATE_*, CORTEX_DECAY_DISABLED, CORTEX_*_BETA) still
  take effect after import. An unconfigured reader raises: returning
  "unset" silently would make every ablation run measure the un-ablated
  system (benchmarks set CORTEX_ABLATE_* without importing __main__).
- core/reranker_model.py: the FlashRank cache lookup, existence check and
  sha256 move to infrastructure/reranker_cache.py behind a seam that
  raises when unwired.
- Both seams join the wiki seams in mcp_server.hooks.wiring
  .wire_composition_root(), the single function every entry point calls.
  It now re-applies its bindings on every call instead of short-circuiting
  after the first, so a seam reset by a test is restored. The per-hook
  copies, benchmarks/lib/_environment_wiring.py, _reranker_wiring.py and
  the import-time wiring in hooks/_telemetry.py are gone;
  benchmarks/lib/_composition_root_wiring.py calls the same function.
- doctor.ensure_reranker_ready() wires through that function; CI's
  reranker preload step calls it instead of reaching into core directly.
- tests_py/benchmarks/test_ablation_runner_wiring.py drives the
  ablation-runner path with a CORTEX_ABLATE_* flag and proves the
  mechanism is disabled.

Fixes #560

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

* test(ablation): the runner wiring test needs psycopg, like the runner (#560)

benchmarks/lib/ablation_runner.py imports db_snapshot, which imports
psycopg; the SQLite-only CI job has no postgresql extra and failed at
import. The PostgreSQL test jobs keep running it.

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

---------

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