Companion to the raw-JSON deprecation warning committed on this branch (adds the
smoke coverage that was meant to land with it).
Migrate scripts/smoke-test.sh from raw-JSON `cli <tool> '{...}'` invocations to
FLAG form for every tool (index_repository / search_graph / trace_path /
get_graph_schema / query_graph incl. all Cypher checks / get_architecture /
search_code / delete_project), with identical results verified against a prior
run; flag form passes the Cypher query as one argv token, so the old
JSON-escaping helper is removed. Add dedicated guards for an integer flag
(--limit / --depth), a bare boolean (--exclude-entry-points), a repeated array
flag (--semantic-query -> JSON array), piped stdin, --args-file, and per-tool
--help (RC 0 + shows a flag; unknown tool -> RC!=0), plus the deprecation guard
(raw JSON warns on stderr; flag form does not). Non-CLI phases (incl. Phase 10
binary security) unchanged. Full smoke: ALL PASSED.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The "tampered arm64 binary is SIGKILLed (137)" premise is empirically false on
current macOS CI runners for an ad-hoc-signed CLI binary -- the binary has no
CS_KILL/hardened-runtime flag, so a tampered code page is not killed: it
executes the garbage and crashes with SIGILL (exit 132, run 28365724001), not
137. (remove-signature and corrupt-blob both ad-hoc re-sign on exec and run to
exit 0.) So no runtime exit code is a deterministic guard here, and
"tamper -> crash" is near-tautological (zeroed code crashes regardless of
signing).
Assert the real, deterministic integrity invariant instead: `codesign
--verify` REJECTS a tampered copy (the CodeDirectory page hashes no longer
match the modified code), while the untampered binary verifies cleanly (10a).
It is a pure userspace hash check -- no tampered code is executed. The copy is
separate, so the original binary stays intact for the 10e re-sign test.
Refs: github.com/garrytan/gstack#997, github.com/nodejs/node#40827
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Refines the previous 10c change on this branch. Garbling only the signature
blob still ran (exit=0 on dry-run 28360363173): since macOS 11 a binary with
a missing/invalid signature is ad-hoc re-signed on exec by newer macOS and
RUNS, so neither remove-signature nor a corrupt blob triggers the kill.
The reliable "tampered binary is SIGKILLed (137)" trigger is tampering the
SIGNED CODE while leaving the valid signature attached: the kernel validates
each executed page against the intact CodeDirectory hash, finds the mismatch,
and kills the process before user code runs. Zero the entry-point
instructions (LC_MAIN entryoff, extracted dynamically) plus a span of early
__text on a SEPARATE copy, leaving the Mach-O header + load commands intact so
it still parses. The original binary is untouched, so the later 10e re-sign
step stays valid. x86_64 keeps remove-signature (code signing is not enforced
there).
Refs: github.com/garrytan/gstack#997, github.com/nodejs/node#40827
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Smoke test 10c (Phase 10 binary security E2E) verifies that an arm64 binary
with an invalid code signature is SIGKILLed (exit 137). It did
`codesign --remove-signature` then ran the binary, expecting the kernel to
kill it. But since macOS 11, a binary with NO LC_CODE_SIGNATURE is ad-hoc
re-signed on exec by newer macOS and RUNS (exit 0) -- so the test went flaky
and then consistently red on updated CI runner images (dry-runs 28350650225
and 28354735368 both failed only here; every other job, including the full
cross-platform test matrix, passed).
Corrupt the signature blob in place instead, leaving the LC_CODE_SIGNATURE
load command intact: AMFI then sees "signed but invalid" and rejects the
binary before any user code runs (deterministic 137). Only the signature
blob is garbled (not the code), so the later 10e re-sign step stays valid --
it replaces the blob and the code is untouched. x86_64 keeps
remove-signature (code signing is not enforced there).
Refs: github.com/garrytan/gstack#997, github.com/nodejs/node#40827
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
mimalloc bumped to v3.3.2 (MI_MALLOC_VERSION 30302), which adds static-CRT malloc override on Windows. Makefile: define the real MI_MALLOC_OVERRIDE=1 ONLY on MinGW (enables the static-CRT override entry points — the generic Windows fix for #424); on Unix keep static-link-order override (defining MI_MALLOC_OVERRIDE there compiles alloc-override.c's forwarding defs and crashes macOS with 'mi_free: invalid pointer' since system libs keep the system allocator). The old -DMI_OVERRIDE=1 was never read by mimalloc source — kept as a prod marker. smoke-test.sh: hard-fail on any 'mimalloc: error' in stderr. Regenerated scripts/vendored-checksums.txt for the new tree (security-vendored.sh passes; no dangerous calls in vendored mimalloc).
The standard linux release binary dynamically links glibc 2.38+ and
GLIBCXX_3.4.32, so it fails to start on Debian 11, Ubuntu 20.04/22.04,
RHEL/Rocky 8/9, Amazon Linux 2, etc. — yet install.sh, the npm and PyPI
wrappers, and the binary's own self-update all fetched it by default,
contradicting the "single static binary" promise.
Point every linux install + self-update path at the fully-static
"-portable" asset (gcc -static), which has no glibc floor. macOS/Windows
are unaffected and unchanged.
- install.sh, pkg/npm/install.js, pkg/pypi _cli.py: select -portable on linux
- src/cli/cli.c: self-update download URL AND checksum archive name both use
-portable on linux (they must match or the update fails checksum verify)
- scripts/smoke-test.sh: assert linux self-update targets the -portable asset
- scripts/ci/check-glibc-compat.sh: new guard — runs the binary inside
debian:bullseye (glibc 2.31) and asserts it starts
- _smoke.yml: run the guard on the portable binary in smoke-linux-portable
Reproduced: standard binary -> "GLIBC_2.38 not found" on glibc 2.31;
portable binary runs cleanly.
The C++ heap-corruption crash only manifests in the production binary (MI_OVERRIDE=1), so the smoke job (which runs the prod binary) is where it reproduces — most reliably on Windows. A ~10k-line templated header exercises the parse-churn path; indexing it must succeed.
Phase 16's FIFO writer-close surfaced as POLLHUP rather than a clean POLLIN+EOF, which the server's poll()-based read loop does not treat as shutdown, so the probe left the process alive and the smoke job failed on every platform. Switch to a plain '< /dev/null' immediate EOF — the server exits reliably (~1s) via its normal getline-EOF path, and it is fully portable (POSIX + MSYS2 bash), so no OS gate is needed. Verified end-to-end: bash scripts/smoke-test.sh reaches 'ALL PASSED'.
Phase 16 of smoke-test.sh launches the stdio MCP server with its stdin held open (a running instance), closes stdin to trigger shutdown, and asserts the process terminates within ~6s — guarding the orphaned-background-process failure mode behind #406 from the prod binary on every platform. POSIX-gated (Windows uses job objects; mkfifo is unavailable on MSYS2).
The cypher unsupported-function check captured stdout, but the CLI prints the parse error to stderr (which cli() redirects into $CLI_STDERR) and exits non-zero, leaving stdout empty — so the assertion always failed once the run reached the smoke stage. Verify the exit status and the stderr channel where the binary actually reports the loud failure. Confirmed locally: full smoke-test.sh passes.
cyp_first_cell built the query_graph JSON by interpolation, so a query with a double-quoted string literal (e.g. replace(f.name, "a", "A")) produced invalid JSON and an empty result (FAIL: replace empty). Escape embedded double-quotes before building the JSON.
#272: '&' is neutralised by the single-/double-quoting of the grep/Select-String/
git commands, so it no longer fails validation. A relaxed validate_search_path_arg
(cbm_validate_shell_arg minus '&') is used for search_code + detect_changes
root_path/file_pattern; all other shell metacharacters stay rejected and
base_branch keeps the strict check.
#282: search_code defaulted regex=false, so 'foo|bar' matched the literal pipe
and silently returned 0 results. The result now carries a warnings[] array that
flags a literal '|' under regex=false (with the regex=true hint), so the trap is
visible instead of looking like a legitimate no-match. (The related invalid-regex
silent-empty case was already fixed in #283.)
Also: every search_code result now reports elapsed_ms, and a perf warning fires
when a search exceeds 5s (also logged as search.slow) so slow calls are visible.
Tests for both issues + the multi-word/invalid-regex no-regression; generous
search_code smoke coverage (basic+elapsed_ms, literal-| warning, '&' acceptance).
Closes#272Closes#282
Wire the Leiden detector into get_architecture via a new 'clusters' aspect.
arch_clusters loads Function/Method/Class nodes + CALLS edges (capped for very
large graphs), runs cbm_leiden, and reports the top-N communities compactly —
each with a dominant-package label, member count, cohesion (internal vs boundary
edge ratio), representative top nodes (by degree), and the packages spanned.
Singletons are skipped to avoid noise. The mcp.c serializer already emitted the
clusters array; it is now populated.
Tests: arch_clusters_basic (two cliques + a bridge -> >=2 connected clusters).
Generous smoke coverage added for the full Cypher surface (labels/type/id/keys/
properties/size/reverse/replace/left/coalesce/substring, NOT EXISTS dead-code,
CASE, unsupported-function error) plus the get_architecture clusters aspect.
Add a single-hop, anchored existence predicate:
WHERE NOT EXISTS { (f)<-[:CALLS]-() } -- functions with no caller
WHERE EXISTS { (f)-[:CALLS]->() } -- functions that call something
Parsed via parse_exists_predicate (reusing parse_node/parse_rel) into a leaf
condition (op=EXISTS, anchor variable, edge type, direction); evaluated against
the bound node with cbm_store_find_edges_by_source_type / _by_target_type. This
is edge-type-specific, so it finds true orphans that in_degree/out_degree miss
(e.g. a node with only a DEFINES edge but no CALLS caller). Multi-hop / nested-
WHERE EXISTS is intentionally unsupported and errors clearly.
Tests cover the dead-code (NOT EXISTS) and has-outgoing (EXISTS) cases; smoke
coverage added. ASan-clean.
Refs: Cypher read suite (EXISTS predicate)
Add an args-list (cbm_func_arg_t) to return items and parse comma-separated
arguments (var.prop or string/number literals), enabling multi-argument scalar
functions in projections:
- coalesce(a, b, ...) first non-empty value
- substring(s, start[, len]) 0-indexed substring
- replace(s, from, to) replace all occurrences
- left(s, n) / right(s, n) leading/trailing n chars
Arguments are freed in free_return_clause (ASan-clean). Unit test
cypher_func_multiarg plus smoke coverage for substring + coalesce.
Refs: Cypher read suite (tier 2b)
Add single-argument string functions to projections — size, length, trim,
ltrim, rtrim, reverse — via the generic function recognizer.
More importantly, change the engine to FAIL LOUDLY on unsupported syntax instead
of silently projecting an empty column. An unknown function call (e.g.
split(...), coalesce(...)) or list indexing/slicing in RETURN/WITH now returns a
clear "unsupported function '<name>' (supported: ...)" error rather than a
valid-looking but blank result — the same silent-empty failure mode that hid the
labels() bug. This supersedes the #373 graceful-resync behaviour (its test is
flipped to assert the error; a new test covers an unknown function in RETURN).
Decision: full Cypher Tier 3 (lists/maps/paths/comprehensions/params — a value
data-model rewrite) is intentionally NOT implemented; clear errors on
unsupported features are the higher-value, lower-risk completeness win for the
read subset agents actually use.
Refs: Cypher read suite (tiers 1-2a + unsupported-syntax hardening)
Add single-argument functions to RETURN/WITH projections, dispatched via a
generic IDENT-call recognizer so new functions no longer need a dedicated lexer
keyword:
- labels(n) -> ["<label>"]
- type(r) -> relationship type
- id(n) -> node/edge identity
- keys(n) -> JSON list of the node's non-null property keys
- properties(n) -> the node/edge properties JSON object
- toInteger/toFloat/toBoolean(x) -> numeric/boolean casts (null on non-numeric)
Previously labels()/id()/keys()/etc. fell into the unknown-function path and
silently projected empty (labels(n) returned ""); they now evaluate correctly.
Regex =~ in WHERE was already supported. Unit tests for each function plus
smoke-test coverage via the live query_graph CLI.
Refs: full Cypher read suite (tier 1 of 3)
The Phase 8 agent-install E2E checked the pre-unification Antigravity paths
(~/.gemini/antigravity/), which broke after the config-path fix. Point the
stub setup at ~/.gemini/antigravity-cli/ and assert the MCP server lands in
the shared ~/.gemini/config/mcp_config.json with AGENTS.md under
~/.gemini/antigravity-cli/. Verified end-to-end (smoke ALL PASSED).
count(DISTINCT x) was a parse error ("expected token type 85, got 9").
parse_aggregate_item now consumes an optional DISTINCT inside the call and
records it on the return item. Both aggregation paths track the set of unique
values per group and emit its size for COUNT(DISTINCT): the RETURN path reuses
the existing collect_lists machinery; the WITH path gains distinct_lists/
distinct_n fields. Plain COUNT and the other aggregates are unchanged.
Unit test: COUNT(DISTINCT f.label)=1 (all same label), count(f.label)=4
(non-distinct), COUNT(DISTINCT f.name)=4 (unique names). Smoke suite adds a
count(DISTINCT) query_graph check.
openCypher node-label alternation was unsupported (parse error after the
first label). parse_node now consumes `:A|B|C` into a single "A|B|C" label
string (mirroring the existing relationship-type alternation). The seed path
unions per-label results (scan_alternation_labels), and target/hop label
filters use label_alt_matches, which ORs over the alternatives. Single-label
matching is unchanged.
Unit test (Function|Module → 5 rows; Function|Class → 4) plus a query_graph
alternation check in the smoke suite. Relationship-type alternation tests
remain green.
openCypher label predicates in WHERE clauses were a parse error
("expected token type 67, got 73"). Parse `var:Label` in the WHERE leaf as
a condition with op=HAS_LABEL/value=Label, and evaluate it against the bound
node label in eval_condition (honoring NOT). Composes with AND/OR and works
in count(...) queries.
Unit test covers true/false/negated label predicates; smoke suite adds a
query_graph WHERE-label check.
The DISTINCT keyword on a WITH clause was parsed (r->distinct) but never
applied, so WITH DISTINCT silently returned duplicate rows. Add a dedup pass
in execute_with_clause that drops projected rows whose full value tuple
duplicates an earlier one (first occurrence kept), gated on wc->distinct.
No-op for the aggregation path (which already collapses per group).
Unit test (4 same-label functions collapse to 1 row; control without DISTINCT
keeps 4) plus a query_graph WITH DISTINCT check added to the smoke suite.
The previous PreToolUse hook gated Grep/Glob/Read/Search with 'exit 2'
on the first call per session, which broke Claude Code's
read-before-edit invariant (issue #362) and could deny tool calls under
upgrade/missing-binary failure modes.
Replace it with a structurally non-blocking augmenter:
- New 'codebase-memory-mcp hook-augment' subcommand reads the hook JSON
from stdin and, for Grep/Glob, queries search_graph (in-process, no
shell) and emits hookSpecificOutput.additionalContext. Every failure
path (no project, short token, missing binary, slow query, timeout)
exits 0 with no stdout — the hook physically cannot block a tool call.
- 300 ms SIGALRM/_exit(0) in-process deadline; 5 s settings.json timeout
backstop. Output is written exactly once at the very end, so a
mid-work timeout yields a clean no-op (never partial JSON).
- Matcher narrowed to 'Grep|Glob' (Read explicitly excluded) for Claude;
Gemini matcher narrowed to 'google_search|grep_search' (excludes
read_file) for the same reason.
- The installed shim is a thin wrapper that delegates to the binary;
legacy filename 'cbm-code-discovery-gate' is kept so existing
settings.json entries upgrade with zero migration. Installer refuses
to embed binary paths containing a double quote (shim injection
defense).
- Per-agent 'old matchers' lists let upsert/remove clean up historical
matcher strings during upgrade.
- Smoke tests (8d/8e/8l) updated to assert the new behavior and
regress-test against re-introducing Read in the matcher or 'exit 2'
in the shim.
- Session reminder text updated: 'always Read a file before editing it'
replaces the prior 'fall back to Read only for text content'.
(cherry picked from commit f72c8e68c4d91e52911a569a967ad782ce5472b2)
The CLI's default print mode (cli_print_mcp_result in src/main.c)
unwraps the MCP envelope and prints the inner JSON directly. The
smoke test was double-parsing as if it received {content:[{text:...}]},
which silently fell through to empty values and failed every assertion
across all platforms (8 occurrences fixed).
- Set APPDATA/LOCALAPPDATA env vars for Windows so cbm_app_config_dir()
and cbm_app_local_dir() resolve to FAKE_HOME paths
- Add Windows (*.exe) branches for Zed, KiloCode, VSCode config checks
- Add macOS branch for KiloCode (was hardcoded to .config/ on all platforms)
- Create platform-correct detection dirs (AppData on Windows, Library on
macOS, .config on Linux) so agent detection + install paths match
- Update skill check from old 4-skill names to consolidated codebase-memory
(old dirs are cleaned up during install since skill consolidation)
On Alpine musl (portable builds), cbm_app_config_dir() needs explicit
XDG_CONFIG_HOME to resolve to FAKE_HOME/.config. Without it, the install
writes to the wrong path and KiloCode/Zed config checks fail.
- Add CBM_SKIP_PERF=1 env var to skip incremental/perf test suite
- CI and Docker test targets skip perf by default (run.sh perf for manual)
- Convert all perf assertions to warnings (log timing, never block)
- Fix store.h anonymous enum in struct (GCC rejects, clang accepts)
- Fix test_store_search.c mkstemp on non-template path
- Add ca-certificates to Docker test image for git HTTPS
- Add cbm_gmtime_r shim in compat.h (Windows gmtime_s wrapper)
- Fix compat.c missing constants.h include (Windows build)
- Fix platform.c _environ redeclaration on mingw
- Rename trace_call_path -> trace_path in smoke/soak/fuzz scripts
- Phase 14: copy binary with .exe suffix on Windows (was creating
non-.exe copy that uninstall didn't remove)
- Phase 14e: check both .exe and non-.exe paths
- Soak latency: exclude index_repository from max query latency
(indexing 377 files is legitimately slow on Windows/MSYS2)
MinGW python3 is a native Windows binary that doesn't understand
POSIX paths like /tmp/foo.json. Piping file content through cat
(which runs in MSYS2 bash and handles path translation) to python's
stdin avoids the issue entirely.
Fixes Windows smoke test 8a and soak baseline collection.
- Phase 14: detect UI vs standard variant from HTTP server contents
instead of hardcoding --standard (fixes UI smoke failure)
- Windows smoke: install zip + coreutils (sha256sum) in MSYS2
(fixes exit code 127)
- Phase 15: UI HTTP server reachability test — verifies root returns
200 and /rpc accepts POST (skips gracefully for non-UI builds)
- Fix switch fallthrough in release.yml (same MSYS2 deps)
Add isatty() checks to prompt_yn() and update variant chooser.
When stdin is not a terminal and no -y/-n or --standard/--ui flag
is provided, print a clear error and exit instead of hanging on
fgets(). Prevents agents from silently blocking when running
install/update programmatically.
Add smoke test 9b-9: verify non-interactive update fails cleanly.
Install command:
- Add cbm_kill_other_instances() to kill stale MCP servers
- Add cbm_macos_adhoc_sign() to sign binary if placed unsigned
Update command:
- Replace skills-only reinstall with full cbm_install_agent_configs()
- Replace external unzip with cbm_extract_binary_from_zip() via zlib
Refactor: extract 10-agent config loop into cbm_install_agent_configs()
called by both install and update.
New: cbm_extract_binary_from_zip() — in-memory zip extraction with
stored + deflate support, path traversal rejection, bounds checks.
4 unit tests. Smoke: add install.ps1 E2E for Windows.
install.sh: one-liner for macOS/Linux — detects OS/arch (Rosetta-
aware), downloads release, verifies checksum, extracts, signs on
macOS, runs install -y for all 10 agents. Supports --ui flag and
CBM_DOWNLOAD_URL env var for testing.
install.ps1: one-liner for Windows — Invoke-WebRequest + Expand-
Archive + Unblock-File (strips MOTW), installs to %LOCALAPPDATA%,
adds to user PATH via [Environment]::SetEnvironmentVariable.
CI pre-signing: add codesign --sign - step for macOS builds in
both dry-run.yml and release.yml, before archiving. Release
binaries now ship pre-signed.
Phase 12 smoke tests: real HTTP download via local artifact server,
checksum verification, archive extraction, binary verification.
Runs only when SMOKE_DOWNLOAD_URL is set (CI provides it).
Phase 13 smoke tests: install.sh E2E — runs full script with local
URL + isolated HOME, verifies binary placed, signed, runs, and
agent configs created.
CI HTTP server: smoke jobs start python3 HTTP server serving the
built binary as a tar.gz/zip archive + checksums.txt. Enables
Phases 12-13 in CI on all platforms.
Update security allowlist: remove system() entry (eliminated),
add cbm_popen for pgrep. Update README with one-liner Quick Start.
Make project a required parameter for all query tools (search_graph,
query_graph, trace_call_path, get_code_snippet, get_graph_schema,
get_architecture, search_code, index_status, detect_changes,
manage_adr, ingest_traces). Removes implicit fallback to session
project or last-opened store.
When project is missing or not found, return error with list of
available indexed projects so agents can self-correct.
Rename delete_project param from project_name to project for
consistency. Fix smoke test trace_call_path depth param name
(max_depth -> depth).
Expand smoke-test.sh with Phase 5 (MCP stdio transport), Phase 6
(CLI subcommands: install/uninstall/update --dry-run), and Phase 7
(MCP advanced tool calls: search_code v2, get_code_snippet).
Add smoke/smoke-amd64 services to Docker compose that build then
run all 7 smoke test phases. Include in run.sh full/all flows.
Add python3-minimal to Dockerfile for smoke test JSON parsing.
Fix Phase 4a shutdown test to use portable background+kill pattern
instead of `timeout` (not available on macOS).
Add --dry-run, --standard, --ui flags to update command. Fix
clang-tidy readability-implicit-bool-conversion in dry_run ternary.
Tests the actual agent handshake path that Claude Code, OpenCode, etc. use:
- 5a-d: initialize → notifications/initialized → tools/list via bare JSONL
- 5e: Full tool call round-trip (index + search) via JSON-RPC
- 5f: Content-Length framing (OpenCode compatibility)
Uses portable background process + kill instead of timeout command
(not available on all macOS configurations).
SS-42