PR B: remove patch-safe audit dead code

[ohjonathan]

Summary

Implements the nine patch-safe PR B findings from #149 on fresh main@d6eca479d5c5d71b2335e3ee2abad4f8d2651e3e. The governing gate was applied to every target: zero package call sites was accepted only after checking package initializers, __all__, re-exports, supported docs, and whole-tree consumers.

The breaking D5b-dead-code-3 removal is not included. This PR retains the 11-name legacy compatibility surface for Ontos 5.x, adds callable DeprecationWarning guidance naming v6.0.0, and keeps PROJECT_ROOT warning-free at import. The audit's original 12-name count included live, supported resolve_config.

Finding-by-finding public-surface checks

• D5b-dead-code-2: _templates had no initializer/__all__ re-export, supported-doc import, or live consumer; removed the private package and package data.
• D5b-dead-code-6: ontos.io did not export obsidian; its only live import was the orphan test; removed it and moved BOM/leading-whitespace coverage to canonical load_document.
• D5b-dead-code-8: the three zero-call wrappers had no initializer/__all__/doc exposure; the two command shims were undocumented internal aliases covered by the maintainer assumption; removed them and repointed tests to canonical core imports.
• D5b-dead-code-9: _create_directories was private, unexported, undocumented, and uncalled; removed it while retaining the rollback-aware initializer.
• D5b-dead-code-10: all six helpers were absent from package exports and supported docs; scanner's alias was explicitly outside __all__; removed all six after whole-tree consumer checks.
• D3b-structure-7: _cmd_export was private and absent from parser/registry dispatch; removed it and added a regression proving bare ontos export still selects _cmd_export_deprecated and creates CLAUDE.md.
• D7-cli-consistency-9: message-only, no import surface; removed the expired v3.4 promise and replaced ontos_init.py remediation with current CLI/Path guidance.
• D5a-repo-redundancy-3: _hooks was private, unexported, and unused; live installed hooks are generated shims that call ontos hook; removed the private package and package data.
• D5a-repo-redundancy-6: repository backups are not package API; deleted exactly 11 tracked .bak files.
• D5b-dead-code-3 (deprecation only, still open): ten functions are re-exported from both ontos and ontos.core, and PROJECT_ROOT remains a direct compatibility import. All 11 stay importable/working; removal remains v6.0.0.

Verification

• 219 focused regressions passed.
• Full suite: 1,585 passed; the approved WAL/SHM flake did not reproduce.
• Exact doctor exit-code regression passed.
• Ontos map and activation: zero errors/warnings; link-check clean; doctor has only the two pre-existing environment warnings (non-Ontos repository hooks and stale PATH ontos), with no new warning and agents freshness green.
• Wheel and sdist built and inspected; neither ships _templates, _hooks, io/obsidian.py, or backups.
• Fresh non-editable wheel install with declared dependencies passed imports, version, removed-module, export, and hook CLI smoke tests outside the checkout.
• llm-dev manifest, schema, review-seat, scope, cardinality, branch, and staging checks passed.
• Whole-tree orphan-import/dead-definition scans, compileall, git diff --check, commit hooks, and clean-worktree checks passed.

Bookkeeping and release hold

The O4 ledger records PR A #167 merged at d6eca47: current main is 15/33 addressed with 18 remaining. This PR implements B=9 for review but does not count them landed before merge. After a verified merge, 9 remain (C=4, D=4, E=1).

Package metadata remains 5.0.0 on this branch. Versioning, merge, tags, PyPI, releases, and issue closure remain maintainer-owned. Do not start PR C until this PR merges and is independently verified.

Refs #149.

[ohjonathan]

Final Codex verification receipt for head feb65a418e7a30771617ded50b4ddb074a2d5143:

• GitHub CI: 6/6 green — Python 3.9, 3.10, 3.11, 3.12, v5-release-gates, and test-non-editable.
• Local full suite: 1,585 passed; approved WAL/SHM flake did not reproduce.
• Focused PR B suite: 219 passed.
• Wheel/sdist inspection and fresh non-editable wheel install passed; retired private packages/module/backups are absent.
• Ontos map/activate: zero errors or warnings; link-check clean. Doctor has only the two baseline environment warnings and reports activation/agents health clean.
• llm-dev manifest/schema/review-seat/scope/cardinality/branch/staging checks passed.
• Whole-tree orphan-import/dead-definition scans, compileall, git diff --check, and commit/push hooks passed.

No release action was performed. D5b-dead-code-3 remains open and import-compatible pending v6.0.0 removal. Awaiting maintainer/Claude independent review and merge; PR C has not started.

[ohjonathan]

PR B review — Claude — approve to merge (no blockers, no majors)

Verified independently in a worktree at the PR head (feb65a4) with a real venv + wheel build. A dead-code sweep is where breaking changes hide, so I re-derived every per-finding public-surface claim rather than trust the report.

The load-bearing check — nothing breaking snuck into a patch

• No public API was removed. Diffed paths.py's public names base (d6eca47) vs head: every symbol present at base is still importable at head — the change is purely additive (deprecation wrappers + private helpers). Deprecate-only, correct for a patch.
• Every removed helper/module is genuinely unreachable. For all 11 removed names (_cmd_export, the six D5b-dead-code-10 helpers, the command wrappers) I ran an exact-token grep across the whole head tree — zero references, static or string/dynamic dispatch. The live _cmd_export_deprecated/_data/_claude handlers that merely share a prefix all remain.
• The paths.py deprecation is real and correctly isolated. External callers get a DeprecationWarning naming v6.0.0 (verified get_logs_dir() fires); PROJECT_ROOT, resolve_project_root, resolve_config stay warning-free; and import ontos + ontos map/activate/doctor all run clean under -W error::DeprecationWarning — no internal caller trips a warning, thanks to the private _get_logs_dir worker that internal code uses instead of the public warn-path.

Everything else held up

• ontos export claude still writes CLAUDE.md; export data dispatches (D3b-structure-7 clean).
• Built the wheel and inspected it: no _templates/_hooks/obsidian entries — packaging correctly updated; test-non-editable green.
• The obsidian BOM coverage genuinely moved to the canonical loader (io.files.load_document, the wired-in scanning path) — a real improvement, not a hollow "moved."
• Activation tripwire (test_doctor_phase4 … passed == 12) green; 159 focused + the new test_paths_v2_deprecation.py pass; full suite 1,585 green (no WAL flake this run); CI 6/6 including 3.12.
• Ledger + [P1-containing] v5.0.1 patch-safe sweep + v6.0.0 path compatibility removal #149 reconciled honestly — PR A's 7 findings + D5a-repo-redundancy-7 checked off (attributed to PR A: align v5 docs and generated instructions #167/d6eca47), PR B's 9 marked implemented with candid "merge/verification pending" notes, and D5b-dead-code-3 explicitly held unchecked for v6.0.0.

One judgment call, surfaced not buried

The four removed command wrappers (export_claude_command, migrate_convenience_command, migration_report_command, verify_document) are the only non-underscore module-level functions deleted — technically importable from ontos.commands.* by a determined external user. They're not re-exported, not documented, and have zero references, so the audit's "unsupported internal aliases" classification holds and removal-in-patch is defensible. Noting it as the single non-underscore-private removal; not a blocker.

Verdict: the cleanest sweep PR yet — no blockers, no majors, ready to merge as a v5.0.1-track patch. Release actions remain maintainer-deferred.