The memory-diagnostics report's priority-4 lane (path-sensitive clang-analyzer,
memory checks only) run over all 111 production files. 21 findings triaged;
the real ones, all cold-path (none can explain #581's per-query residual):
LEAKS
- mcp get_architecture: scope_path leaked on the missing-store early return
(REQUIRE_STORE frees only `project`); allocate after the gate.
- pass_definitions: cancellation mid-extraction leaked the pass-owned result
cache including already-extracted entries; mirror the end-of-pass cleanup.
- store package-boundary scan: the row-scan abort path freed the node arrays
but not the boundary accumulators or their duplicated package strings.
- cbm quarantine set: a duplicate path line leaked the replaced value (and a
fresh key copy -- the table borrows key pointers); a partial strdup failure
leaked the surviving half. Reuse the stored key for duplicates.
- pass_githistory: unchecked malloc/strdup -- an OOM dereferenced NULL and a
failed strdup leaked the index cell. Allocate before claiming the slot.
NULL/UB
- cli config subcommand: NULL argv with nonzero argc slipped the guard (the
inner `argv &&` shielded only the help comparison) into argv[0].
- store bfs_multi: a negative max_results broke out before any row was
written, then freed fields of an unwritten negative-index slot. Clamp.
- pass_calls emit_http_async_edge: the service-pattern call sites pass a NULL
target behind a hand-duplicated URL predicate; a drift between the copies
turned target->id into a null deref. The callee is now total.
- sqlite_writer: both leaf-array OOM paths left leaf_count stale with a NULL
array, walking pb_finalize_* into leaves[0]; consistent empty state routes
them to the existing root=0 failure return.
HARDENED (invariants true but invisible to path-sensitive analysis)
- Leiden CSR + aggregate arrays, SCC adjacency: calloc + endpoint guards, so
a future degree/collection miscount degrades benignly instead of UB.
- SCC cycle fill: the ncyc==0 no-slot invariant made local.
RECORDED FALSE POSITIVES (no code change)
- yaml sequence starts (loop bound == alloc bound), cypher agg arrays (same
count both sides), mcp read_message ch (assigned by fgetc each iteration),
pkgmap clean buffer, mcp csize (Tarjan: ncomp>=1 when nverts>=1), vendored
verstable x2.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
GATE + LANES (user decision: runner cost accepted)
- make lint-mem (local triage) and lint-mem-ci (gating: vendored-filtered,
any remaining finding fails). The gate is green because every false
positive above was restructured for provability -- calloc'd fill-cursor
arrays, explicit Tarjan invariant, zeroed buffer tails, min-1-element
allocations -- never suppressed.
- make diag: pinned newest-LLVM ASan/UBSan lane with straighter stacks.
- CI: lint-mem job (_lint.yml) and test-diag job (_test.yml), both on the
pinned LLVM 22 apt toolchain. Cost disclosure: roughly +25-40 min and
+25-60 min (ccache-warm) per push respectively.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Keep the live database visible until a synced temporary generation can
replace it. Preserve destination sidecars on replacement failure and use
UTF-8-safe Windows file operations.
Signed-off-by: Nikita Bige <wargloom@gmail.com>
cbm_writer_open used a raw ANSI-CP fopen for the hand-rolled SQLite
writer - the one file-creating call on the dump chain without a
UTF-8-to-wide conversion. On a non-ASCII Windows profile
(C:\Users\Kovacs Janos) extract and resolve succeeded but the dump
failed with pipeline.err phase=dump: fopen could not create graph.db
under the profile-derived cache dir while cbm_mkdir_p (already wide)
had happily created the directory around it. Routed through cbm_fopen,
matching #700 (pass readers) and #973 (canonicalization); POSIX is
byte-transparent.
New Windows guard test_non_ascii_cache_dump.py indexes an ASCII repo
into a non-ASCII CBM_CACHE_DIR and requires a query_graph readback
with Function count > 0 - proving the DB was written to and reopened
from the non-ASCII cache, not merely that no error surfaced. The
existing non-ASCII guard only varied the repo path against an ASCII
cache, which is why this class went unseen.
The USERPROFILE-sourced env encoding question (Layer 2 - _environ is
ANSI-CP, not UTF-8) is deliberately not bundled; it needs verification
on a real Windows box and will be filed separately if the guard alone
does not settle it.
Closes#996
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Three code paths install a brand-new DB file where a previous
generation lived without removing the destination's -wal/-shm:
the pipeline page writer (cbm_writer_open), artifact import (which
cleaned the TMP file's sidecars but not the destination's), and
cbm_store_dump_to_file (whose comment wrongly asserted stale sidecars
'become stale and get recreated'). SQLite validates a WAL against the
sidecar's own header/checksums — not the main file — so a crashed
session's leftover WAL is replayed ON TOP of the freshly installed
file at the next open, splicing old-generation pages into it.
New shared helper cbm_remove_db_sidecars (compat_fs, wide-path safe on
Windows) called at all three install points.
Reproduce-first: dump_install_ignores_stale_wal_sidecar follows the
issue's recipe (hot-copy a live WAL, clean close, restore the copy,
install generation 2, reopen). RED on the unguarded code — the replay
clobbered the fresh generation entirely (fresh row unqueryable);
GREEN with the cleanup. Non-vacuous: asserts the hot WAL is non-empty
before the copy.
Closes#897
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Distills PR #770 (graph-buffer dedup key) and completes the edge-uniqueness
contract it left partial: the contract lives in THREE places, and changing
only the buffer ships databases that violate their own UNIQUE constraint
(PRAGMA integrity_check: non-unique entry in sqlite_autoindex_edges_1).
A single 'import { A, B } from ./lib' produced ONE IMPORTS edge: the graph
buffer dedups edges on (source_id, target_id, type) and merge-replaces
properties on collision, so the second symbol silently overwrote the first.
pass_calls.c, pass_usages.c, pass_semantic.c and pass_lsp_cross.c parse one
local_name per IMPORTS edge for cross-file resolution, so the dropped
symbol's calls failed to resolve too — not just "who imports X" queries.
Changes, kept in sync across all three sites:
- graph_buffer.c (from #770): make_edge_key() folds local_name into the
dedup key for IMPORTS edges only; all three key call-sites updated.
Hardened beyond #770: EDGE_KEY_BUF bumped to 256 and oversized
local_names are re-keyed with an FNV-1a hash of the full name instead
of being silently truncated (two long names sharing a prefix must not
collide back into one edge).
- store.c: edges gains local_name_gen, a VIRTUAL generated column
(IMPORTS -> coalesce(json_extract(properties,'$.local_name'),''),
else '' — NOT NULL because NULLs never conflict in a UNIQUE index);
uniqueness widened to UNIQUE(source_id, target_id, type,
local_name_gen) and the insert upsert's conflict target matches.
init_schema probes pre-#768 DBs (no local_name_gen) and fails the
open: SQLite cannot ALTER a table constraint in place, and an
unopenable DB already takes the existing repair path — full index
deletes + rebuilds, artifact import refuses and falls back to a
reindex. Read-only query opens skip init_schema and keep working.
- sqlite_writer.c/.h: dump DDL matches the widened schema; the hand-built
sqlite_autoindex_edges_1 comparator and entry builder include the
local_name column; CBMDumpEdge carries local_name extracted via real
JSON parsing (yyjson) so index entries match json_extract's unescaped
values exactly, per the idx_edges_url_path precedent.
- artifact.h: CBM_ARTIFACT_SCHEMA_VERSION 1 -> 2 so old binaries refuse
artifacts carrying the widened schema (their 3-column conflict target
can no longer prepare against it).
Tests (reproduce-first, all red on the unfixed code):
- gbuf tier: multi-symbol import -> 2 IMPORTS edges; long-local_name
truncation guard.
- store tier: distinct local_name coexists as 2 rows, same local_name
still upserts, non-IMPORTS dedup unchanged.
- writer tier: dumped DB passes integrity_check with 2 sibling imports
and exposes matching local_name_gen values.
- end-to-end: TS fixture through the real pipeline -> 2 queryable
IMPORTS edges AND integrity_check ok; with only the buffer half of
the fix this test still fails on integrity_check, proving the schema
half is required.
Closes#768.
Co-authored-by: Alexandros Pappas <11921291+apappas1129@users.noreply.github.com>
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The hand-rolled dump writer stored index cells fully inline regardless of payload size. SQLite's format spills index payloads above the max-local threshold (16,422 bytes at the 64 KB page size) to overflow pages, so a long key written inline makes the reader interpret key bytes as an overflow page number: PRAGMA integrity_check reported 'invalid page number 0x43654C6C' (ASCII from the key text) in idx_nodes_name on elasticsearch (very long Section names), and name lookups on that index silently returned nothing. write_index_btree now rewrites oversized cells (varint + local prefix + overflow chain via write_overflow_pages) before page building; promoted separators carry their chains with them. Reproduce-first: sw_long_index_keys_overflow (20 KB name; integrity_check failed pre-fix, ok post-fix). Also escapes the remaining raw text interpolations in DATA_FLOWS route props and HANDLES handler QNs (the ~51-edge malformed tail after 6c04ab7).
Whitelist find_first_descendant_by_kind and find_first_descendant_of in recursion_whitelist.h (bounded AST-depth DFS, like the existing r_collect_imports entry), and narrow two cppcheck-flagged variable scopes in sqlite_writer.c: use w->project at its single use, and fclose the value-copied wc.fp after free(w) instead of a pre-captured fp.
The CI lint (clang-format-20) flagged formatting violations across these files (pre-existing drift plus the new extraction code). Reformat to satisfy the check; no logic changes.
Split cbm_write_db's monolithic build into an incremental API:
cbm_writer_open / cbm_writer_append_nodes / cbm_writer_finalize. Node
rows are written to the table B-tree across append calls via a
persistent page builder, so callers can flush and free node batches
(including the heavy properties column) without materializing every
record at once. Everything after the nodes table — edges, vectors,
metadata, indexes, and the sqlite_master page — is emitted at finalize,
as before.
cbm_write_db is now a one-shot wrapper (open, append all nodes,
finalize) producing byte-identical output; the full test suite and
PRAGMA integrity_check confirm the on-disk format is unchanged.
Format drift had accumulated across recent commits (the dry-run lint enforces clang-format-20, which had not run on these commits yet). No functional changes — whitespace/layout only, verified by a clean cppcheck + clang-format + NOLINT lint-ci pass.
98d5cac silently dropped index cells that exceed a single SQLite page,
which is the correct semantic (the index B-tree has no overflow page
mechanism, unlike the record B-tree fixed in #175). But silent drops
make the failure mode invisible — a caller hitting deeply nested
namespaces or very long file paths gets a partial index with no
indication anything was skipped.
Add an fprintf(stderr) at the skip site reporting the cell length and
its index, matching the existing logging style in this file (lines 311,
1305) so the dropped cells are observable for diagnosis. Consistent
with the cbm_write_db: prefix used by surrounding warnings.
write_index_btree() flushed the page buffer whenever the next cell
didn't fit, on the assumption that a freshly-initialised page would
always accept any cell. That invariant fails for index cells whose
payload (qualified_name, file_path, etc.) is larger than a full
SQLite page — after the flush, pb_cell_fits() is still false but the
code calls pb_add_cell() anyway. The subsequent content_offset
underflow corrupts the page header and the next write triggers
SIGBUS on large repos (observed on a Ruby codebase with ~215K nodes).
Re-check pb_cell_fits() after the flush and continue past cells
that still don't fit. Index entries whose keys exceed a full page
can't be stored and are not expected to survive the writer anyway —
the rest of the index is correctly preserved and the indexer no
longer crashes. Record overflow pages (#175) already covers the
record-btree side of this same shape of bug.
When a single record payload exceeds 65KB (max_local=65501), the writer
now splits it across overflow pages per SQLite's B-tree spec instead of
underflowing the content_offset and corrupting memory.
Closes#139, closes#187.
Based on #175 by dLo999.
Co-Authored-By: Dustin Obrecht <dustin@kurtnoble.com>
- Parallelize pass_similarity and pass_semantic_edges via worker pool with
thread-local edge buffers; sequential final merge since gbuf is not
thread-safe. Adds cbm_lsh_query_into() as a thread-safe variant with
caller-provided candidate buffer.
- Add activatable profiling subsystem (CBM_PROFILE=1 env or --profile flag)
for step-level timing of extract, resolve, corpus build, vector phases,
and sqlite dump. Zero overhead when disabled.
- Fix cbm_index_mode_t enum mismatch between pipeline.h (FULL=0, MODERATE=1,
FAST=2) and discover.h (FULL=0, FAST=1). mode=fast silently no-op'd
fast-discovery filtering because discover.c compared against the wrong
value. Linux kernel fast mode went 1:40 -> 3:11 as a result; now back to
1:40. Broaden the filter guard to mode != CBM_MODE_FULL so MODERATE and
FAST both get aggressive discovery.
- Clamp cbm_sem_combined_score output to [0, 1]. The proximity multiplier
returns up to 1.10 as a same-file boost which could push the final
cosine score above 1.0.
- Short-circuit semantic scoring when MinHash jaccard >= 0.95. Exact
near-clones are already emitted as SIMILAR_TO edges; returning 0 here
avoids flooding SEMANTICALLY_RELATED with cross-service copy-paste
boilerplate and frees the edge budget for genuine vocabulary-bridged
relations.
- Validate search_graph semantic_query as an array of strings and return
a clear error for a single-string input. Update the tool description
to spell out the requirement explicitly with an example.
- JSON-escape user-controlled strings (callee names, call arguments,
URL paths, import local_name) in call/argument properties. Introduces
cbm_json_escape() in foundation/str_util.
- Skip SQLite pending_byte_page (file offset 0x40000000) during raw page
writes in sqlite_writer to avoid corrupting databases that cross the
1 GiB boundary.
- Migrate pretrained vector blob from UniXcoder (51K tokens) to
nomic-embed-code (40856 tokens x 768d int8). Includes the extraction
script under scripts/extract_nomic_vectors.py.
Major quality improvement: replace random index vectors with pre-trained
Nomic nomic-embed-code token embeddings. Tokens like 'error' and 'exception' now start
with similar vectors (learned from millions of code repos) instead of
arbitrary random projections. Co-occurrence enrichment adds project-specific
context on top.
Architecture:
- vendored/nomic/code_vectors.bin: 37.7MB raw int8 vectors
- vendored/nomic/code_vectors_blob.S: assembler .incbin (instant build)
- vendored/nomic/code_vectors.h: extern declarations + pretrained_vec_at()
- vendored/nomic/code_tokens.h: 40856 token strings (575KB)
- semantic.c: cbm_sem_random_index() now looks up pretrained vectors first,
falls back to sparse random for unknown tokens
- CBM_SEM_DIM raised from 256 to 768 to match Nomic nomic-embed-code
Also: RRI (Reflective Random Indexing), code pattern vocabulary injection,
120+ abbreviation expansions, callee/caller/body token enrichment,
label filter (Function/Method/Class only) in vector search SQL.
Binary size: 136MB → 169MB (+33MB from embedded vectors).
Search quality: keyword queries return relevant error-handling functions.
Domain-specific keyword queries return the expected functions.
Vector search pipeline (end-to-end):
- store.c: cbm_cosine_i8 custom SQLite function (int8 dot product with
sqrt magnitude), registered at store open time
- store.c: cbm_store_vector_search() builds merged query vector from
keywords via base RI vectors (xxHash), int8-quantizes, runs SQL query
with JOIN nodes ON node_id = id for metadata
- mcp.c: search_graph gains semantic_query param (array of strings),
returns semantic_results alongside regular results
- sqlite_writer.c: fixed build_vector_record to include node_id in
record body (matches build_node_record pattern)
- mcp.c: use yyjson_mut_obj_add_strcpy (not add_str) to avoid
use-after-free when vector results are freed before JSON serialization
Quality note: base RI vectors at query time don't capture co-occurrence
enrichment — results are moderate quality. Storing enriched token vectors
would improve this significantly (future work).
Lower thresholds to best-practice values:
cognitive-complexity: 250 -> 25 (industry default)
statements: 400 -> 200
lines: 800 -> 400
Add NOLINTNEXTLINE to 168 functions that currently exceed these thresholds.
Each suppression will be removed as the function is split in subsequent
commits. Zero net behavioral changes.
Also: extract execute_with_clause from cypher execute_single.
sqlite_writer.c pb_build_interior: final root-level sep_cell
allocations were not freed. Each cbm_write_db call leaked 84 bytes.
Detected by ASan on Linux CI with 155 incremental test iterations.
Also fix CI timing: use MAX_TOOL_MS (15s) for perf assertions,
skip timing on full re-index operations (CI runners are slower).
Enforce WarningsAsErrors: '*' with zero suppressions of entire check categories.
All non-FP warnings fixed at source; true false positives get per-instance NOLINT
with reasoning. Fixes include: braces around statements (1679), isolate declarations
(75), explicit casts for multilevel pointer conversions, missing includes, function
parameter documentation via NOLINT, and proper NOLINTBEGIN/NOLINTEND nesting.
Complete C implementation of the indexing pipeline (src/), parallel worker
pool, graph buffer with merge support, SQLite writer, and 1893-test suite.
Linter setup: zero warnings from clang-tidy (all checks enabled, no NOLINT
suppressions), cppcheck, and clang-format. All issues fixed at source —
proper headers for external linkage, GROW_ARRAY macro restructured to
eliminate type parameter, null-deref paths guarded, named intermediates
for suspicious-argument checks.
Martin Vogel