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fix(codebase): hub git routing + write refactors - #16
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- codebase(action=git) resolves the real project_root and dispatches log/history/branch/file to dedicated git tools instead of a non-existent log path (fixes 'Path does not exist: .../log'). - write_tools safe_delete counts real usages via find_all_references (was find_references, which missed cross-file callers -> false '0 usages'). - write_tools move infers a valid dotted module relative to project root instead of a Windows absolute path (fixes 'from D:\... import ...'). - replace/insert dry-run already guarded by apply=False (regression added). - docs: AGENTS.md §2 synced to registered tool set; KNOWN_ISSUES updated. Regression: tests/test_codebase_hub.py, tests/test_write_tools.py (67 passed).
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…11) (#40) * style(search): strip trailing whitespace in graph_adapter * fix(release): align version to 3.5.0 in extension.toml and __init__ * docs: sync version references to 3.5.0 stale_detector flagged 20 outdated version strings across 17 docs (en/ru/zh). Updated to the pyproject version; stale_detector now reports 0 drift. * test(e17): add signal-value experiment harness Measures what execution-derived TESTS edges buy an LLM across four tasks. - e17_extract.py: AST extraction of functions/tests (fixes qualified-name match that returned FUNC NOT FOUND for every class method). - e17_pilot_experiment.py: specificity- and complexity-selected panel, unique/foreign/coverage-matched decoy, edge-case and impact questions. - tooling: line-budget prompt shards for isolated subagent generation, blind test-hidden judging, objective impact recall/precision. - report v1-v4: reasoning tasks hit a ceiling (B never beats A); impact ('which tests cover F') is decisive for the signal (A=0.00, B=1.00). - 13 extraction tests including adversarial cases. Result recorded in AGENT_DIARY.md and KNOWN_ISSUES.md. * test(e17): validate TESTS-signal as a verifier via mutation testing Negate the first single-line if inside 10 panel functions, run the graph-linked tests (arm B) and coverage-matched decoy tests (arm D), restore via git checkout. - B killed the mutant 6/10, D 0/10 (Fisher exact p=0.011). - 4/10 linked tests did not catch a strong mutation (weak assertions, e.g. TestCypherLexer asserts only len(tokens) > 0). - Conclusion: the signal identifies verifying tests far better than decoys, but its value is bounded by assertion strength, not coverage. * test(e17): profile verification strength across multiple mutations 10 functions x 4 mutations (negate-if, flip-compare, bool-flip, int+1, str-append); every graph-linked test and decoy run under every mutant. - 24 tests profiled; decoy tests killed 0/104 mutants (control clean). - kill-rate predictors (Spearman): assertion specificity rho=+0.54 p=0.006, assert count rho=+0.47 p=0.019, density/LOC not significant. - What an assertion compares against matters more than how many it has. TESTS edge = reach; mutation kill-rate = verification. * test(e17): scale strength profiling; AST proxies do not predict kill-rate 24 functions (providers/mcp excluded), 55 tests, 4 mutations each; split by function; decoys killed 0/55. - v6 correlation (exact_compare rho=+0.54) did NOT replicate: train rho=+0.13, held-out rho=-0.01; rule precision 0.59 / recall 0.67. - AST features (assert count/density/specificity/LOC) do not predict whether a test catches a behaviour change; TEST_VERIFIES needs real mutation runs. - Report marks v6 CORRECTED; history preserved. * docs(known-issues): archive autosynced experiment entries * fix(search): revive idle embedder, unblock hot-reload in search Two independent causes of search_code >15s timeouts (2026-09-22): - llama_runner watchdog unloads the embedder after EMBEDDER_IDLE_TIMEOUT (120s, free RAM) but RemoteEmbedder never brought it back -> :8080 connection refused (WinError 10061) -> per-chunk retries -> timeout. Add LlamaRunner.is_port_up()/ensure_embedder_started() and revive the server once on embed failure, before per-item retries. - _maybe_hot_reload awaited a full reindex inside search_code; a batch of new/changed files (22) pushed the call past the 15s budget even with a live embedder. Run it as a deduped background task. - Also fix the inverted model key in the (currently unreferenced) LlamaRunner.embed (bge-m3 -> DEFAULT_EMBEDDING_MODEL). Tests: tests/test_embedder_idle_recovery.py (10). * docs(experiments): record E6 commit-gate and E7 symptom-index eval * docs(experiments): finalize E7 eval (3 models, arrival-symptom NONE 10/10) * feat(graph): add quiet-break isolation gate (delta A+B) Detect commits that silently isolate a graph node, read-only (git diff + persisted PropertyGraph, no index mutation). Absolute zero-inbound-CALLS is unusable (1535/4081 = 38% of repo), so two delta signals: removed_last_caller (a symbol still defined loses its last caller) and new_orphan (a newly added function nothing calls). Exposed as graph_query(action=isolation) / CLI; fail-open (unavailable/empty) when git or graph is absent. Controls: unit 10/10, real-git E2E 4/4, CLI 1899ms 0 false positives. * feat(cli): redact credentials at delivery boundary Delivery notes (hooks -> python -m src.cli -> model context) bypass the commit secret-gate, so a key pasted into a note as evidence would leak into every agent context the note fires on. Add an in-house prefix-anchored redactor (src/core/redact.py) and apply it at the single CLI choke point (success and error JSON). Anchored on structural prefixes, not entropy, so paths, commit hashes and digests survive byte-identical. Not a security boundary (novel/split-line formats pass) - documented as such. Design credited to Tom Jones, crystal-memory scripts/redact.py (Apache-2.0, not vendored). Tests: 8/8 (unit + CLI integration). * feat(delivery): add anti-numbing restraint for advisory notes Repeated identical advisory notes numb the reader (Tom Jones crystal-memory; our E3/E4). Add src/core/restraint.py: a findings signature (kind+symbol+file) with a per-project cooldown and 2^strikes backoff, state in data_root (atomic replace). Opt-in via graph_query isolation kwargs={restraint:true}; blocking gates never use it (a blocked commit is a hard stop, not nagging). Tests 4/4 (22/22 with gate+redact); CLI E2E: call1 deliver, immediate call2 suppressed (cooldown 597s). * docs(experiments): record E11 frozen list vs new arrival index Blind mapper against Tom's catalogue arrival index (tjonesit/crystals @3e30ed2): the dispositional arrival symptom (#16 agent won't use tools) now reaches family A in 5/5 runs including both VALID runs (longcat-2.0, qwen3.7-plus, controls 6/6). deepseek x3 invalid (NC3 UI-spacing lure, same NONE-control failure as E7). New risk noted: the arrival layer can manufacture a false positive on an adjacent domain. * docs: clean-state verification 44d451f (1800 passed, all gates green) Local-clone clean state via verify_clean_state.sh --no-clone on committed revision 44d451f: 1800 passed / 0 failed / 13 skipped / 98 deselected (822s); lock-drift negative control PASSED; guard inventory ALL PROVEN (3); revision gate VALID. Note: when a branch is not pushed, the default GitHub clone verifies origin, not this branch - clone the local repo and use --no-clone. * test(graph): make TESTS-signal fixture platform-independent test_graph_stage_e4 hardcoded file_path D:/Project/... which is not absolute on POSIX, so get_tests_for_symbol normalized it to <root>/D:/... and found no node -> 0 covering tests. Passed on Windows, failed on ubuntu (2 tests). Build absolute paths from tmp_path.as_posix() instead; fixture is now platform-independent. * docs: record CI green on PR #40 (ubuntu+windows+clean-state) Fix 808864c turned the ubuntu CI green; full run success. Only remaining red is GitHub Advanced Security (Copilot Autofind), which fails with CAPIError 400 model-not-supported on GitHub's side, not our code. * feat(opencode): add commit-time gate hook (stale block + isolation advisory) Project-local opencode plugin: on git commit, run stale_detector (block on objective doc drift) and graph_query isolation (advisory; graph gate has FP risk). Advisory uses before-stash/after-deliver by callID (E8 lesson). CLI invoked as python -m src.cli with cwd=project (CLI ignores --project). Env switches MSCODEBASE_PY/STALE_GATE/ISOLATION_GATE/GATE_LOG. Activated after Zed reload; global install is out of workspace and needs explicit approval. * fix(opencode): invoke CLI via node:child_process, not plugin context In opencode 1.18.23 the plugin factory context does not provide a callable shell helper (docs describe v2 where it exists as BunShell). The hook loaded (init logged) but threw "TypeError: ... is not a function" on the shell call. Call python through node:child_process.execFile with an argv array (no shell quoting) instead of the context shell. node:fs already worked, so node builtins are available in the plugin runtime. * docs: record opencode gate hook live verification Fresh init after restart; git commit --dry-run -> stale drift=0, isolation count=0. Negative control (staged new_orphan added in a separate git add step) -> isolation count=1 and the advisory note delivered into the command output; test file removed, tree clean. Note: the hook runs before the command, so git add && git commit in one command leaves the file unstaged at hook time and the gate cannot see it. * fix(docs): verify_references no longer crashes on a lone dollar in backticks auto_update_docs(action=verify) raised IndexError "string index out of range": the empty-content guard ran before the $ prefix was stripped, so a lone $ (or $ ) in backticks left content empty and content[0] blew up. Re-check for empty content after stripping $. Adds a regression test. * feat(docs): deterministic L1 doc-reference checker (near-zero FP) The old verifier collected only definitions and scanned venv via rglob, so it reported 1366 broken with ~3% real (params/fields/stdlib). Replace the reference check with src/core/doc_reference_l1.py: vocabulary = identifiers + string literals from src/tests/scripts/tools (+root scripts); scope = live docs (root docs minus ledgers, docs/** minus archive/generated/research/blog/ISSUES/ investigations); whitelist stdlib/typing, external APIs, env vars, model names, commit scopes. auto_update_docs(action=verify) now delegates to it. Effect (measured): broken 1366 -> 0. Also fixes WISDOM naming a non-existent _symbol_resolver (actual: _build_symbol_resolver). Tests 4/4. Limitation: a stale tool name that still appears anywhere in code/tests is masked; tool names need a registry check, not a vocabulary check. * docs(experiments): record E13 test-time measurement (xdist ~15%) xdist -n 4: 1817 passed in 169s vs 200s serial (~15%), no failures. Not worth default complexity; CI cold clean-state (~13m) is dominated by install/caches, not CPU. Named next levers: cache pip in clean-state and investigate test_temporal_facts_generator (~42s). * docs: sync tool counts to code (65 = 32 core + 16 intel + 13 inline + 4 dev) Authoritative count derived from code (server_tools.py tool_classes, tools_reg.py and dev_tools.py decorators, server_tools.py inline decorators): 65 registered tools. Fix contradicting numbers in README (61/66), AGENTS (64, 31 core) and docs/{en,ru,zh}/ARCHITECTURE (64/61/58/46, 28/31/20 core); describe the visible set via the MSCODEBASE_MCP_TOOLS allowlist instead of a stale magic number. L1 checker clean (0 broken); tests 12/12. * docs(readme): semantic audit fixes against code Verified claims against code and corrected: tests badge 1856 -> 1889 (_count_tests), last-updated date, DI services 18 -> 14 (di_container.py has 14 add_singleton calls), tests 1773 -> 1889, and the tool-count line (32+16+13+4=65, +execute_script -> 66). Confirmed correct: 29 EdgeType members and 13 structural_search patterns. Open: AGENTS.md lists get_repo_map/... as "not registered" while they are registered tool_classes (hidden by allowlist) and README lists them - needs a decision. * docs(agents): semantic audit fixes against code Fixed: source-of-truth path src/core/intelligence_layer.py does not exist -> src/core/intelligence/layer.py; CI matrix "(3.10-3.12)" -> Python 3.14-only. Confirmed correct: RuntimeCoordinator/can_execute, ProjectContext.capture() (project_context.py:164), apply_file_move (indexer.py:659), root files. Open: the "Not registered (consolidated)" block lists get_repo_map/get_hotspots/ verify_action/get_task_status etc. as not exposed, but they are registered tool_classes (hidden by the default allowlist) - needs an owner decision. * docs+fix: resolve "not registered" tools; correct server_tools log counts Mechanism: only core tool_classes in the MSCODEBASE_MCP_TOOLS allowlist are registered via mcp.tool(); intel(16)/inline(13)/dev(4) are always registered. So the AGENTS claim was right in spirit (hidden -> tool not found) but the list was wrong (verify_action/get_task_status are in the default allowlist; bootstrap_ pipeline was missing). Rewrite the block as "Hidden core tools (default allowlist)"; add a visibility note to README; fix the startup log hardcode in server_tools.py (intel 14->16, inline 12->13) that printed "62 total" while 65 register. * docs(architecture): semantic audit fixes (en/ru/zh) against code - Layer 2 "Bridge" marked deprecated (code: not used, LSP server removed 2026-07-20). - server.py "~220 lines" -> 68 (actual line count). - core "30 files" -> 54 top-level (123 incl. subpackages). - DI container "15+/18 services" -> 14. - README: lsp_main.py "does not work" -> "removed" (file deleted). Confirmed correct: tool counts 32/16/13/4=65 and module paths. * docs(architecture): fix services/labels/tool-group counts against code - remote_embedder described as ONNX-only -> llama.cpp GGUF primary with ONNX/LM Studio/Ollama fallback. - "15 node labels" -> 16 (NodeLabel members). - DI "Registered Services (11)" -> 14 (add Path, Indexer, GitUrlSourceFactoryKey). - Tool groups: Intelligence 14 -> 16 (add restore/supersede), Lifecycle 3 -> 4 (add get_action_receipt). --------- Co-authored-by: MSCodeBase Agent <mscodebase@intelligence.local>
ManSio
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Sep 26, 2026
…production) Blind mapper via opencode (longcat-2.0 x5, qwen3.7-plus x3, deepseek-v4.1-flash x3), isolated dir, MCP off, --pure, tools denied. Valid 5/11; in all valid runs #16 -> NONE (arrival symptom unreachable); the only failure is the same known false positive (#11 Safari/CSS -> a-generated-document-is-unverified), concentrated in deepseek (0/3 valid). Qualitative reproduction of E7 confirmed; numeric rate NOT reproduced (5/11 vs ~10/11) because --variant was not pinned. Raw runs and manifest under results/recovered_e7/.
ManSio
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Sep 26, 2026
Replace ad-hoc PowerShell+Tee with scripts/f4_blind_run.py (subprocess argv-list, UTF-8, ANSI-strip); --variant is required so an unpinned run fails loudly. Rerun with --variant high: valid 10/11 (longcat 4/5, qwen 3/3, deepseek 3/3), controls 6/6 in all valid, #16 -> NONE everywhere. The earlier 'deepseek 0/3' was an unpinned-budget confound, not a model property. Pitfall #19 added to the registry.
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Summary
Fixes 4 real bugs in the \codebase\ hub (write-actions dry-run, move import, safe_delete callers, git log routing) and syncs AGENTS.md §2 tool registry.
Fixes