The bulk writer builds each interior level greedily: it fills a page with
separator cells until the next one no longer fits, uses that child as the
page's right child, and starts the next page after it. When a page filled
up exactly at children[child_count - 2], only the last child was left, so
the next (and last) page of that level was written with ZERO cells and
just a right-child pointer.
SQLite rejects a non-root page with nCell < 1 as SQLITE_CORRUPT the moment
a cursor descends into it (getAndInitPage). Because that page is always the
last one of its level, the failing descent is the rightmost path -- exactly
what the coverage-shadow wipe takes: "DELETE ... WHERE project = ?1" with
"<project>::missed", a key that sorts after every row of "<project>". The
publish then failed with "coverage_shadow_wipe: database disk image is
malformed". It needs an index with more than one interior page on a level
(large graphs or long keys) AND the page-fill boundary landing on the one
bad position, which is why it looked scale-dependent and repo-specific;
the same DBs also fail PRAGMA integrity_check.
When a page fills with exactly one child left, give its last cell back, so
the next page holds one cell plus the last child as its right child. The
removed bytes are zeroed, keeping the output deterministic.
Test: sqlite_writer::sw_interior_level_never_ends_with_empty_page writes
2..120 rows with 12000-byte names (one and two interior levels) and runs
the wipe-shaped DELETE through idx_nodes_name; rows 31-35, 61-65 and 91-95
failed with SQLITE_CORRUPT before the fix. Real input: 41 generated
markdown repos with long headings indexed by v0.11.0 -> 5 databases fail
the "::missed" seek and integrity_check; with the fix 0 of 41.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
cbm_gbuf_dump_to_sqlite() emitted gbuf.dump regardless of the writer's
result, so a run that published nothing still logged node and edge counts
as if it had worked, and the failure reached the user only as the generic
"Pipeline failed. Check repo_path exists and contains source files."
The writer's temp -> final rename in publish_writer_output() returned a
bare ERR_WRITE_FAILED. #1628 taught cbm_rename_replace() to translate the
platform error into errno so callers could report why, and wired up the
stage -> final rename in pipeline.c. This is the other rename on that
path, and it is the one that runs first.
Preserve errno across the cleanup in every publish error branch. That
includes cbm_writer_open(), where the cleanup unlinks a file that was never
created: without the save it leaves ENOENT behind, so a directory that
denied the create is reported as a missing path — the #1620 case, stated
wrongly. Read the value in graph_buffer.c before the profiling macro can
clobber it, and report gbuf.dump_failed with the return code and that errno.
A sticky append failure clears errno rather than attach a reason it does not
have, and the field is omitted when there is none. No logging is added
inside internal/cbm/, which has none today.
Tests cover both halves: the dump reports a failure instead of a summary,
the writer names its truncation reason, and the publish rename's errno
survives a cleanup that itself fails.
Refs #1620, #2001.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012FxkVF773gDGNmBmsLnzN7
Signed-off-by: juan Carlos Estrada Montoya <junk151516@users.noreply.github.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>
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).
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>
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).
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