When an agent greps for a symbol that the graph knows, the PreToolUse
augmentation (Grep, Glob and Bash searches) lists the matching symbols. It now
closes with one line that is cbm's own statement, outside the untrusted symbol
block, naming the graph tools for the usual next question:
[codebase-memory] For these symbols, trace_path lists callers and callees,
get_code_snippet returns the exact source, and search_graph finds related
symbols by name.
The line carries no repository-derived value and is stated as facts, as Claude
Code asks of hook context. It is appended at the string's real end into
reserved room: the list loop's offset can run past its cap when a row is
truncated, so appending at that offset could have written past the buffer.
Searches without a hit, errors and non-search events are unchanged.
Refs #509
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Claude Code defers every MCP tool behind ToolSearch by default: at session
start the model sees only tool names and server instructions, while Grep and
Read are always loaded. Codex does the same and shows the server instructions
as the namespace description of the deferred tools. Agents therefore reached
for grep before the graph tools were even loaded (#509, discussion #2025).
- tools/list: search_graph, trace_path and get_code_snippet carry
_meta["anthropic/alwaysLoad"] = true (a documented per-tool hint), so the
structural discovery path loads upfront while the other 14 tools stay
deferred. About 4.6K characters of schema; clients that do not know the key
ignore it, as MCP reserves _meta.
- Server instructions (default profile) now state, keywords first and as
facts, which structural questions the graph answers and where grep fits
better: 309 -> 999 characters, within Claude Code's 4,096-character cut.
- SessionStart/SubagentStart: the untrusted-metadata label now covers the
graph-derived project name only. Wrapping the routing sentences too told the
model to treat cbm's own guidance as data. The other sentences are unchanged;
sanitization is unchanged.
The initialize byte budget is raised deliberately from 512 B to 1.5 KiB (1,188
bytes now); tools/list stays within its 21 KiB budget (20,938 bytes).
Refs #509
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Nondeterministic Windows reds came from races on _config.db:
test-windows-guards section_start_status_port / daemon_lifecycle ("the
daemon did not accept the UI configuration"), section_churn_stability
("could not load saved runtime settings"), the windows-2025 release
smoke whose `--ui=true --port` server exited about 5 s after start
(Phase 15, read as "no embedded UI assets"), and section_crash_recovery
("the stale daemon state never cleared").
- Every _config.db connection now waits out a committing writer
(cbm_runtime_settings_wait_for_writers: one busy handler, logs
config_db.busy_wait once per busy wait, a 3 s bound for a wedged
holder). Startup's 50 ms window let a daemon's routine commit end
unrelated CLI starts; cbm_config_open and the UI load had no wait at
all, so a concurrent commit failed the daemon's UI save and made the
load keep defaults.
- A process killed mid-write (crash, taskkill /F, power loss) left a hot
rollback journal that the read-only settings reads cannot roll back
(SQLITE_READONLY_ROLLBACK). Every later command then failed with
"could not load saved runtime settings", permanently. Settings startup
and the UI load now recover once through a read-write open that rolls
the interrupted write back (config_db.hot_journal_recovered); a failed
recovery is reported with the journal path and stays fatal.
- write_value no longer rewrites an unchanged value. The upsert fired the
revision trigger, so every `daemon start` on a UI build committed and
locked readers out although nothing changed.
- `daemon start` and the stdio server wait for the set_context and
set_ui_config replies within their startup budget instead of the 1 s
probe budget (MAIN_CONNECT_TIMEOUT_MS) that decided the command
whenever the daemon's save ran long.
Tests, red on 8df0639c and green here:
- runtime_settings suite: three single-threaded lock tests (a log sink
commits the held lock when the waiter logs config_db.busy_wait, so no
test depends on a duration) and two hot-journal tests (a portable
fixture snapshots the database and its journal mid-transaction and
checks the journal is hot before the code under test runs).
- tests/windows/test_daemon_stability.py: new section
start_port_waits_for_settings_writer holds the lock against a real
`daemon start --port` and releases it on events; the crash section
now prints the status output it saw.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
A workload's environment names the services it talks to
(PRODUCT_CATALOG_SERVICE_ADDR: productcatalogservice:3550, a URL, a
<svc>.<ns>.svc name); the graph had no edge for it, so the service topology
of an application was invisible.
A Kubernetes workload or a compose service now CONNECTS_TO the Service its
containers' environment addresses, with {via: env, key, container} -- never
the value:
- the address: the host of a URL or of host:port, a <svc>.<ns>.svc name in
the value, or the whole value when the key names an address (*_ADDR,
*_ADDRESS, *_HOST, *_URL, *_ENDPOINT, *_URI) and it is a bare DNS name; a
templated value, localhost or an IP addresses nothing, and only service DNS
forms count (svc, svc.ns, svc.ns.svc...), never another domain's host
(cbm_env_address, shared by both sides);
- Kubernetes: a reference resolved like every other one -- a Service of the
same bundle, in the named namespace or the object's own;
- compose: a service of the same file; a variable without a value takes the
project's .env, whose values compose expands against the lines before them
(CART_ADDR=cart:${CART_PORT}) -- the dotenv reader does that now too.
Consumers: trace_path's topology mode, the CLI's edge list and the README
(which also gains DEPLOYS and the env join of the previous commit).
Measured on 17 infrastructure repositories: 129 edges, every one correct by
hand; an independent reading of the values finds 133 pairs repo-wide, the 5
without an edge belong to another bundle or namespace.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
`cli list_projects` with no arguments blocked forever whenever fd 0 was a
pipe nobody closes: an ssh session's stdin, or a Node child_process.spawn
parent that never calls stdin.end(). That is the #1359 deadlock again.
The #1359 gate only skipped the stdin read for a tool whose schema
declares NO properties; #1181 then gave list_projects optional paging
properties, and the read came back for exactly the callers #1359 fixed.
It showed up as a 25-minute stall in the Windows smoke's Phase 1b over
ssh, and it is the same in v0.11.0.
The gate now asks what stdin is (terminal, regular file, or stream) and
what the tool needs:
- terminal: never read (unchanged);
- no properties: never read (unchanged);
- optional properties only: a regular file (`cli list_projects < args.json`)
is read, since a file always reaches EOF; a stream is not, and the call
runs with `{}` exactly as an interactive one does;
- any required property: file or stream, the documented
`echo '<json>' | cli <tool>` channel, unchanged; the bare call cannot
succeed without it.
Only list_projects is optional-only today; the other 16 tools all require
an argument. Piping JSON into list_projects is no longer read; flags,
--args-file and `< file` still are.
Proof (macOS, the release-tree binary vs this one, isolated runtime dirs):
- held-open pipe: `list_projects` hung until killed at 20 s -> returns in 0.4 s;
- `list_projects < args.json` ({"format":"json"}): JSON on both;
- `printf '{"project":"nope"}' | cli index_status`: same "project not
found" on both.
Tests: the #1359 schema seam now takes the stdin kind; new
cli_optional_argument_tool_never_reads_stream_stdin (fails before: the
old gate admitted a stream for list_projects) and
cli_stdin_kind_classifies_file_and_pipe; the whole-table sweep checks
file and stream separately and asserts it really covers an optional-only
tool.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Doc-section -> code candidates (doc_link_candidates, #2574/#2610) are the
documentation-in-the-graph feature of this release. They now run by
default for full indexes and not for moderate or fast ones; an explicit
`doc_candidates` argument, or a `doc_candidates` setting the user set,
overrides the default either way in every mode.
- pipeline: the switch is unset/on/off; unset means on only when the
effective mode is full.
- MCP: forwards only an explicit choice (argument, then a user-set config
value) to daemon jobs and workers; daemon auto-index and watcher/UI jobs
now carry a user-set value too (their workers have no config, so
`doc_candidates false` was ignored there).
- fast + doc_candidates on runs the semantic pass's corpus phases and the
doc phase only: candidates, and still no SIMILAR_TO or
SEMANTICALLY_RELATED edges.
- config: `doc_candidates` joins the config key table (default `auto`);
`config set doc_candidates ...` was refused as an unknown key before.
README, docs/CONFIGURATION.md and the MCP schema describe the default.
Proof (macOS arm64, django fb11376):
full 11,304 rows · moderate 0 · fast 0 · full+off 0 · moderate+on 1 ·
fast+on 1 (moderate/fast discovery skips docs/) -- nodes and edges are
identical between on and off in every mode; fast+on adds 0 semantic
edges.
- New tests (RED on the old code): pipeline
pipeline_doc_candidates_default_follows_mode,
pipeline_doc_candidates_explicit_wins_over_mode,
pipeline_doc_candidates_fast_on_legacy_incremental; mcp
tool_index_repository_doc_candidates_follow_mode,
tool_index_repository_doc_candidates_forwarded_only_when_explicit;
daemon_application
daemon_application_programmatic_index_forwards_set_doc_candidates.
- mcp 374 passed (4 Windows-only skips), daemon_application 73 passed,
pipeline/store_arch/cli/runtime_settings/index_policy/pipeline_frozen
green on the release tree.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The doc<->code candidate scoring (#2574, doc_section_worker in
semantic_edges) scores every documentation section against the functions
that share a key term with it, key terms being those held by at most
funcs/20 functions. Its cost therefore grows with sections x functions.
Measured on 11 corpora (10-09 main vs 4d9592b5, semantic_edges): under a
second up to ~100k functions, +12.6 s on java (325k), +14.6 s on csharp
(451k), +174 s on the Linux kernel (784k functions, 28k sections), almost
all of the kernel's regression against v0.11.0.
A new boolean setting, doc_candidates (default true), and an optional
index_repository argument of the same name switch the scoring off: no
candidate rows are stored and nodes and edges are unchanged. The argument
wins over the setting. The index handler resolves the value once and
passes it to a daemon job or supervised worker as an argument, the same way
as the resource policy, so every route sees one decision; the session
auto-index reads the setting. With the switch off, a delta-route reindex
replaces the candidate rows it would otherwise keep, so turning it off
leaves no stale candidates. The default output is unchanged.
Tests (each fails on its assertion when the switch has no effect):
- pipeline_doc_candidates_off_stores_none_and_keeps_graph: no rows, same
node and edge counts as the default run, which has rows;
- pipeline_doc_candidates_off_clears_rows_on_delta: a closure-repair
reindex with the switch off removes the earlier rows;
- tool_index_repository_doc_candidates_switch: argument false -> none;
setting default -> rows; setting false -> none; argument true over
setting false -> rows.
Proof, release-built binaries on macOS arm64 (M5 Pro 18c/48 GB):
- django, main 4d9592b5 vs this change with defaults: nodes (63,441),
edges (307,584) and doc_link_candidates rows (11,304) hash-identical;
- django with doc_candidates false: nodes and edges hash-identical, no
candidate rows;
- Linux kernel with doc_candidates false: semantic_edges 17.9 s (191.9 s on
main, 17.6 s before #2574), whole index 210.9 s (v0.11.0: ~234 s), no
candidate rows.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Brings in #2596 (MSan: hidden uninitialized reads) and #2068 (CodeAtlas
web).
README: main's CBM Atlas line and this branch's infrastructure-as-code
line are both kept.
tools/list metadata: main and this branch each stayed under the 20 KiB
discovery budget, but together they reached 20,809 bytes. The branch's
wording is shorter now (search_graph kind/namespace, one hint per trace
mode: 136 bytes less), and the reviewed budget is 21 KiB so the
topology/deploy/run modes keep their usage hints.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Normalize Windows cache paths when reporting runtime settings and resolve
Git executables before spawning history queries. Keep executable lookup
results per thread and cover the ownership contract deterministically.
Support Git 2.43 while denying history-query network transports, and close
the activity database on daemon startup failure so Windows can clean up.
Validation: 463 native macOS tests, 421 Windows tests, 44 MSan UI tests,
and focused canonical lint passed. Production-only revert checks confirm
the repaired failures.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Reconcile the complete Atlas and Lens stream with current main while retaining both histories. Preserve architecture functionality, current process and watcher safeguards, test infrastructure, and dependency security updates. Add coverage for Git-environment isolation combined with child-local overrides.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
On macOS the signed-candidate preparation folded every step into one
boolean, so each failure printed the same line: "signed update candidate
preparation failed". A full /tmp read exactly like a broken codesign. That
is what a cli test hit on 2026-10-09, while a multi-GB index was filling a
nearly full disk.
Each step now records why it failed, and the update prints, for example:
error: signed update candidate preparation failed while writing the
unsigned candidate: No space left on device
The staging functions in activation_transaction.c keep the errno of the
failing write (or sync, close, read) through their cleanup, so a caller can
name it. The non-macOS path adds the OS error to its existing "failed to
stage verified update" line (POSIX only; Windows reports through
GetLastError). A failed fingerprint of the staged file now gets its own
message instead of "...: activation transaction completed".
A test seam makes the next staging write fail with a chosen errno. The new
test cli_update_names_the_failing_staging_step_and_os_error fails without
the cli.c change and passes with it, and checks that the old executable
stays in place. Also checked on real input: with /tmp on a small volume
that fills between two updates, the update prints the line above.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The README's Graph Data Model named USES_TYPE, MEMBER_OF and
CONTAINS_PACKAGE, which nothing emits, and left out 14 labels and 18
edge types that real indexes hold -- among them the infrastructure ones
(Resource is listed, but not Chart, Process, EnvVar, INFRA_MAPS or
DEPENDS_ON) and Variable, Section, Field, Struct, OVERRIDE, INHERITS,
TESTS_FILE and the CROSS_* family. The skill text `install` writes for
agents carried the same CONTAINS_PACKAGE and no infra edges, so an agent
following it queried an edge that never exists and did not learn the
ones that do.
Both lists now name exactly what is produced: checked against the
labels and edge types of 17 infrastructure repositories and 86 local
indexes, plus a quoted producer in the sources for the types those
indexes do not exercise (Trait, Constant, DATA_FLOWS, CROSS_*). Against
the same data the old README had 29 mismatches, the new one none.
The edge summary also describes INFRA_MAPS (Service -> the workloads its
whole selector selects, one namespace) and DEPENDS_ON (Helm chart ->
declared charts with their repository; go.mod / requirements.txt ->
external Package), and the infrastructure bullet names Helm charts and
Terraform / OpenTofu files.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
A reference written in a doc comment is extracted with the definition it
documents (internal/cbm/doclink.c; the C# scanner doclink_cs.c) and
resolved per file in the pipeline (src/pipeline/doc_links.c,
doc_links_cs.c, doc_links_msbuild.c). A reference that names a definition
of the repository with certainty becomes a MENTIONS edge from the
documented definition (the File node for a file-level comment) with the
properties via, syntax, tier, line and count. Any other reference becomes
a row of the new doc_link_unresolved table with its reason: missing,
ambiguous, external, test_only_target, graph_gap, unparseable or
below_bar_tier. Nothing is guessed. index_status reports the layer in a
doc_links block.
C# binds a cref by the compiler's lookup rule: the first scope with the
name decides, a cref never binds an inherited member, System is outside
the repository. Assemblies come from project files, and MSBuild global
usings (<Using>, ImplicitUsings, Directory.Build.props/.targets, imports,
conditions) are evaluated from the project files' content as data the
indexer has already read; the layer opens no file. Two declarations of a
name in different assemblies make the reference ambiguous.
Each file's scope is stored line-free with its LSP surface ("dl"), so an
incremental run re-resolves the files a change can reach and falls back
to a full run for a change that can re-route references anywhere (a
project file, a global using, a deleted file).
The scanner and the resolver treat the repository as untrusted input:
bounded nesting, no input-driven recursion, work that grows linearly
(held by test seams, never by a clock), no silent limits, and a damaged
or foreign stored scope fails closed.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The test-impact engine selects tests by walking the graph, so it can only
be as right as the graph. Three gaps made it wrong:
One identity for a definition's mutually exclusive variants
- A definition written once per #if/#else branch, per #[cfg], per
platform file (foo_linux.c / foo_win.c, platform directories) or per Go
build tag is ONE node. The graph buffer keeps every variant's span in a
`variants` node property (definition labels only), so a change in any
variant maps to the definition.
- Extraction now sees definitions inside conditional blocks where it
skipped them: C++/C#/ObjC class members under #if (one cursor walk,
conditional block types per language in lang_specs), Elixir defs under
if/unless, Fortran .F90/.F95/.F03/.F08, Rust #[cfg] twins (no more
`name#cfg(...)` QNs that lost every call), C platform files and
directories (non-static file-scope functions).
- Haskell: the vendored scanner reads only an #if group's first branch.
The grammar stays upstream; every further branch is parsed as its own
same-length view (cpp_branch_views.c) and adds what the raw parse
missed. haskell/bytestring: no new partial parses, +27 functions,
IMPORTS 322 -> 329, 131 definitions with variant spans.
- Incremental closure repair re-parses every file of such a definition
when one of them changes (variant partners through DEFINES), so a
repair equals a full index.
No cross-language name guesses
- A name-only resolution (unique_name, suffix_match, qualified_suffix,
field_type_hint, and same_module across files that only share a path
stem) never binds a symbol another language defines.
- Bash imports are the files a script sources: every top-level command
was read as an import of its name (`set -e` imported "set", bound to a
TSX method in 137 scripts here).
- This repository: cross-language CALLS 5,916 -> 5,091; the remainder are
C/C++ pairs, builtins and same-stem module collisions (recorded).
SPAWNS edges (per language, like the HTTP client patterns)
- A call that starts a program (subprocess.run, exec.Command,
child_process.spawn, posix_spawn, system, Process.Start, Command::new,
... about 30 languages, through the file's own imports) gets a SPAWNS
edge to a Process node named after the program (literal first word, or
<dynamic>) instead of a CALLS guess. No target resolution. Both
resolvers ask at the same point (parity test).
The engine follows the graph
- Seeds map changed lines through every variant span; a test written
once per #if branch is one test; when a change reaches a non-test
`main`, the tests that spawn processes are reached too (the process
runs main, and main reaches everything).
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Require --delete-indexes for automatic or noninteractive index removal.
Keep the separate terminal prompt with a default of retaining indexes,
and preserve dry-run and guarded activation ordering.
Refs #2200
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
An agent in a checkout whose directory name differs from the repository
name (git clone .../repo_name.git some_name) could not find the indexed
project. The installed skill only said "list_projects - check if project
is indexed", so Codex and Copilot guessed the project from the repo name,
got "project not found" and stopped using the graph. Passing the working
directory did not help whenever it was not exactly the indexed root: a
path was only ever turned into the path-DERIVED name, which misses a
checkout indexed under an explicit name (the stored identity, see #1660)
and every directory below an indexed root.
Fix:
- mcp: a path-shaped project keeps the derived name when an index exists
under it (unchanged fast path); otherwise it resolves to the indexed
project whose stored root_path owns the directory. The deepest owning
root wins; two projects owning that root stay unresolved, so the
not-found error lists every project instead of guessing. Reuses the
list_projects identity reader and the canonical-path containment helpers.
- mcp: the project-not-found hint says how to pick the project (the name
whose root_path contains the working directory, or that absolute
directory; never a repo or folder name), so an agent that guessed can
recover.
- cli: the SKILL.md every skill client installs (Codex, Copilot and the
rest), the shared agent instructions and the Aider CLI instructions say
the same thing.
Proof (dev binary, synthetic HOME; repo_name cloned as some_name and
indexed by path; a second checkout other_dir indexed with name=my-alias):
before: project=<other_dir> -> project not found
project=<some_name>/pkg -> project not found
after: project=<other_dir> -> my-alias (index_status agrees)
project=<some_name>/pkg -> the some_name project
unchanged: the checkout root path and the explicit name resolve; the
unindexed sibling some_name_x stays not found; a guessed "repo_name"
stays not found and now carries the how-to-pick hint.
Tests:
- mcp tool_project_path_resolves_owning_project_issue1690: an explicitly
named root and its subdirectory resolve; normal naming and similar
names (some_name2, some_name_x) are not confused; two owners of one
root are never guessed; a guessed repo name gets the hint. RED 3x
before, green after, RED again when the production change is reverted
(the hint check also goes RED on its own revert).
- cli cli_guidance_resolves_project_by_root_path_issue1690: pins the
instruction in the skill, agent-instructions and Aider variants.
Fixes#1690
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
A project indexed from a directory that is not a git repository was never
refreshed after its first index: init_baseline classified it is_git=false
and poll_project/check_changes returned early for it forever, so the graph
silently went stale. The comment in init_baseline even claimed such folders
were "polled as a plain directory", which was never true.
Add an opt-in config key, watch_non_git (default false, read once at daemon
startup like watcher_enabled). When on, a non-git root is polled on the
existing adaptive cadence (cbm_watcher_poll_interval_ms) by a tree
signature: the indexer's own cbm_discover walk (same skip lists, .gitignore
stack and .cbmignore), sorted by path and folded over (relative path, size,
mtime). A changed signature takes the existing reindex path with the same
commit-after-success discipline as the #937 dirty signature. The baseline
leaves the signature "unknown", so the first poll reindexes once
(at-least-once, covering edits made while the daemon was down).
Runaway guard: only files discovery would index enter the signature, so
cbm's own .codebase-memory output (built-in skip) and the cache directory
(pruned by absolute path) can never make a finished reindex look like a
new change; a scratch folder under an unrelated dirty repository is polled
on its own files and never inherits the ancestor's dirty state.
cbm_file_info_t gains mtime_ns, filled from the stat discovery already
performs, so the signature needs no second stat per file and stays
UTF-8-correct on Windows (discovery's wide stat).
Docs: README and docs/CONFIGURATION.md now say non-git roots are not
watched by default and document watch_non_git. The staleness signal in
index_status is left to #1561's freshness object. Refs #1948.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Codex rewrites its [mcp_servers] tables whenever it edits MCP servers
itself (`codex mcp add`, its MCP settings, wrappers such as Orca that
drive it) and drops comment decor on the way. From our managed block it
keeps the table but loses the begin marker, omits `args = []`, and leaves
the end marker as an orphan below whichever table follows. Reproduced
with codex-cli 0.153.4: after `codex mcp add orca -- /bin/echo hi` the
file holds an unmarked
[mcp_servers.codebase-memory-mcp]
command = ".../codebase-memory-mcp"
env_vars = ["CBM_CACHE_DIR", "CBM_RUNTIME_DIR"]
and a stray `# <<< codebase-memory-mcp MCP <<<` under [mcp_servers.orca].
Every later install then failed with op=mcp_install on a table cbm itself
had written, twice over: cbm_toml_remove_legacy_table refused the orphan
marker as malformed, and its owned-shape check predated env_vars (#1562,
#1664), so even without the orphan the table counted as foreign.
cbm_toml_remove_legacy_table now drops a lone orphaned marker line in the
same atomic write (we are the only author of those markers, #1558; only
that line is removed, nothing is guessed) and treats env_vars naming only
CBM_CACHE_DIR / CBM_RUNTIME_DIR as part of the owned shape. A table with
any other key or forwarded name is still foreign and left byte-identical,
and a foreign table keeps the file untouched, orphan included. The scan is
split into toml_strip_legacy_table + toml_legacy_classify_assignment so
the entry point reads the file, heals, strips and writes once.
The same helper backs the Grok Build install, which gains the same
self-heal.
Tests: cli_upsert_codex_mcp_adopts_codex_rewritten_table uses the exact
bytes Codex produced; config_toml_legacy_remove_adopts_owned_env_vars_only
pins the env_vars boundary (owned names adopted, any other name foreign).
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Why: the activation rendezvous is per OS account, so an install or update
run under another HOME / CBM_CACHE_DIR (a sandbox, a second profile) meets
the account's live daemon at the same endpoint. The daemon's
activation-shutdown handler verifies only the requester's build, never its
cache, so the CLI's scope decision is the only thing that tells "my daemon"
from "someone else's". That decision drained the cohort unless the active
cache was positively DIFFERENT: a busy session group (another activation or
a session start held it, so the active identity was never read) and an
unreadable active cache both fell through to "ours", printed "Stopping
active CBM sessions" and shut the daemon and every session behind it down.
Fix (user decision 2026-09-28, "unknown = foreign, keep it"): only a
positive match may drain. cli_activation_resolve_scope returns
CLI_ACTIVATION_SCOPE_ACTIVE only for an OK admission (exact identity, cache
included, or an empty group) or for a conflict whose cache fingerprint
equals this activation's. BUSY and a blank active cache now return the new
CLI_ACTIVATION_SCOPE_UNCONFIRMED, handled like a foreign cohort: no lock is
taken, no drain request is sent, the mutation proceeds, and the audit log
records "quiesce_skipped: active cohort ownership unconfirmed (...)". A
read-only status probe names the daemon that was left (pid, version) and
the notice says how to stop it: close its sessions, then run
`codebase-memory-mcp daemon stop`. The confirmed paths are unchanged: a
normal self-upgrade still drains its own daemon, a clearly foreign cache is
still left alone.
Proof (product binaries; private CBM_RUNTIME_DIR; an own permanent test
daemon started from the same build under a host HOME/cache; a sandbox
HOME/cache on the same runtime dir; the cohort maintenance gate held by a
second process, i.e. a busy session group):
- origin/main: "Stopping active CBM sessions and operations for
install...", the test daemon was stopped (daemon status: not running),
and the install still failed (rc=1 after 23 s, "could not be stopped
safely").
- this change: "Leaving the running CBM daemon untouched (pid 76713,
version dev): this install could not confirm that it serves the cache
this install targets (the session group was busy, so its cache identity
could not be read)." The test daemon kept running with the same pid and
the install completed (rc=0, 10 s).
A lifetime record whose cache field is zeroed is refused (UNSAFE) by both
builds with the daemon kept; that path never drained and is unchanged.
Tests (cli suite; fixture daemon in a private runtime dir; sandbox HOME):
- cli_install_foreign_home_unreadable_cohort_cache_keeps_host_daemon
(the new seam cbm_cli_set_activation_scope_cache_unreadable_for_test
blanks the observed active cache fingerprint)
- cli_install_foreign_home_busy_cohort_keeps_host_daemon (the maintenance
gate is held through the product's own lock-directory handle)
Both were RED 3x on origin/main for the right reason (the host daemon was
drained: ASSERT(host_serving)), are green with the fix, and turn RED again
when the fix is reverted. Controls stay green:
cli_install_into_host_namespace_still_drains_host_cohort (confirmed same
cache: drained, as before) and
cli_install_{skip_binary,binary}_into_foreign_home_never_drains_host_cohort
(clearly different cache: kept, as before).
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Why: arming the hook-augment deadline opens its breadcrumb log with
O_CREAT. The path came from raw getenv("HOME") as
"%s/.cache/codebase-memory-mcp/logs" in 1 KiB buffers with no length
check. A HOME near 1 KiB therefore created a file at the cut-off name
(".../logs/hook-augme") on every hook call, and a longer one created a
cut-off directory. The hook also ignored CBM_CACHE_DIR, which every
other cbm component honours for its cache and logs. The index skip log
had the same defect in its CBM_INDEX_LOG override: an override longer
than 1 KiB was copied in unchecked and opened "wb", which created or
truncated the file at its cut-off prefix and reported that name as the
run's logfile.
Fix: the breadcrumb log now resolves through cbm_resolve_cache_dir()
(CBM_CACHE_DIR, else HOME, else USERPROFILE, plus the default) to
<cache_dir>/logs/hook-augment-timeouts.log. Every snprintf into the
1 KiB buffers is checked, including the one for the CBM_HOOK_TIMEOUT_LOG
override. A path that does not fit means no breadcrumb, and the logs
directory is created only for a path that fits. The hook still exits 0
(it never fails the agent's hook call) and allocates nothing new. The
CBM_INDEX_LOG override gets the same check: an override that does not
fit writes no logfile and warns index.logfile_path_too_long, and the
index still completes. With a normal HOME the log stays where it was.
Proof (dev binary, synthetic roots, isolated CBM_RUNTIME_DIR, no-op
Bash payload on stdin; "created" = find over the synthetic root minus
the pre-made HOME/cache chains):
- 980-byte HOME. Before: exit 0, plus three directories and a file at
the cut-off name <HOME>/.cache/codebase-memory-mcp/logs/hook-augme
(1023 bytes). After: exit 0, nothing created.
- CBM_CACHE_DIR=<root>/cache. Before: the log landed under HOME.
After: <root>/cache/logs/hook-augment-timeouts.log.
- 1000-byte CBM_CACHE_DIR. After: exit 0, nothing created.
- Normal HOME: <HOME>/.cache/codebase-memory-mcp/logs/
hook-augment-timeouts.log before and after.
- 1096-byte CBM_INDEX_LOG via `cli index_repository`. Before: a file
at the 1023-byte cut-off name, reported as the logfile. After: status
indexed, skipped_count 1, no logfile, nothing written.
Tests: RED 3x on the unfixed code for the reasons above, green with
the fix, RED again with the fix reverted:
- cli: cli_hook_augment_log_long_home_creates_no_cut_path,
cli_hook_augment_log_honours_cache_dir, plus the positive control
cli_hook_augment_log_default_location_unchanged (green before and
after).
- index_resilience: index_long_log_override_writes_no_cut_path.
The fixtures sit under link-resolved temp roots: the kernel bounds the
expanded path, so under macOS's /tmp -> /private/tmp link a near-1 KiB
path can be neither created nor probed, and the bug stays hidden.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Add focused galaxy tracing, edge filters, organic cluster layouts and cached
graph exploration with compact architecture and impact summaries.
Make the browser-local agent explain the current selection proactively,
and add a Config panel with persisted daemon overrides, shared browser
preferences and a reference for external configuration inputs.
Validation: 182 focused frontend tests and TypeScript passed. Reused the
recorded production build and 485 passing native checks on unchanged
source. The pre-existing capped-layout loading-note test failure remains
documented separately; the full local CI ladder was waived.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Three detection defects kept `codebase-memory-mcp install` from
configuring agents people run, and made it configure one they never
installed.
OpenCode without a config file or a CLI on PATH (#1167, #1180).
OpenCode was detected only from its global config file or directory,
OPENCODE_CONFIG_DIR, or an `opencode` found on PATH. It now also counts
as installed when its data directory exists: ~/.local/share/opencode on
every OS, %USERPROFILE%\.local\share\opencode on Windows
(opencode.ai/docs/troubleshooting, "Storage"; the same page names it as
the global config location of older installs). The OpenCode CLI and the
Desktop app both create it -- the Desktop's bundled opencode-cli server
uses the same XDG paths (anomalyco/opencode packages/core/src/global.ts
creates the config and data dirs at startup;
packages/desktop/src/main/sidecar.ts only redirects XDG_STATE_HOME) --
so detection no longer depends on PATH. The install target
~/.config/opencode/opencode.json(c) -- %USERPROFILE%\.config\opencode
on Windows per the same docs page -- is unchanged and right for CLI and
Desktop alike. A PATH longer than 4 KB, which hides every CLI from
find_in_path(), is handled separately by PR #2381.
Hermes home on Windows (#1180). Native Windows Hermes -- the install.ps1
CLI, the MSIX package and the Desktop app -- defaults HERMES_HOME to
%LOCALAPPDATA%\hermes and falls back to a legacy ~/.hermes only while
that directory is absent (NousResearch/hermes-agent
website/docs/user-guide/windows-native.md, "Data layout";
apps/desktop/electron/data-paths.mjs, resolveDesktopHermesHome). cbm
probed and wrote ~/.hermes only, so a Desktop install was never detected
and a Hermes found on PATH got its config.yaml and skill in a home it
never reads. On Windows the home now resolves to
<home>/AppData/Local/hermes unless only ~/.hermes exists, using the
home-derived AppData convention of the existing Zed, goose, Kilo and VS
Code probes; detection, install and uninstall all follow it. HERMES_HOME
still wins, and macOS/Linux keep ~/.hermes.
Claude Code from a bare ~/.claude (#1180). Any ~/.claude directory
counted as a Claude Code install, so a user who only had the folder got
hooks, skills and MCP entries for a client they never installed.
Detection now needs what Claude Code itself leaves behind: settings.json
in the config dir, .claude.json in the home (in CLAUDE_CONFIG_DIR when
set), or the claude CLI.
Proof on macOS against synthetic HOME/cache/runtime dirs with a minimal
PATH (`install --dry-run --skip-binary`, then a config-only install):
bare ~/.claude main: Claude-Code fix: none
~/.local/share/opencode only main: none fix: OpenCode
In the OpenCode case the fixed install writes the codebase-memory-mcp
entry to ~/.config/opencode/opencode.json; main writes nothing. Controls
(a launched Desktop layout, a real Claude user) are detected by both.
The Windows Hermes home is covered by a platform-parameterised resolver
test that runs on every host plus a _WIN32-bound end-to-end detection
and plan test.
Tests (cli suite, 335 passed): seven new tests; five fail on main three
times out of three (the _WIN32-bound Hermes test and the look-alike
control are green on macOS by design). Reverting the Claude+Hermes half
and the OpenCode data-dir probe separately turns exactly their own tests
red. Nine existing Claude fixtures that used a bare ~/.claude as the
install marker now write .claude.json; two Hermes tests and smoke-test
8x expect %LOCALAPPDATA%\hermes on Windows.
Refs #1167Fixes#1180
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
cbm_toml_upsert_managed_block and cbm_toml_remove_managed_block treated
everything between the "# >>> codebase-memory-mcp MCP >>>" markers as
ours: install replaced the whole span with the fresh block, uninstall
deleted it, and the conflict check skipped that same span. When our block
ended ~/.codex/config.toml, Codex Desktop appended its own tables below it
while the closing marker stayed the last line, so [mcp_servers.node_repl],
[desktop] and the [marketplaces.*] tables sat inside the markers. The
0.10.4 -> 0.11.0 upgrade deleted all of them, together with the
startup_timeout_sec the user had added to our own table.
The span is now read as TOML sections, each classified against the tables
the block declares:
- owned: a declared table (the k-th [[element]] of a declared array). The
keys the block writes are replaced; every other key, comment and blank
line in it stays in the table.
- attached: a sub-table of a declared table, such as
[mcp_servers.codebase-memory-mcp.env]. It is part of our server entry
and stays with it; outside the markers it would collide with the next
install.
- foreign: any other table, moved byte for byte and in order to just after
the closing marker, so from then on the markers bracket only our entry
and later appends land outside them.
- lead: lines above the span's first table, moved above the opening
marker, where they keep the table they belong to.
Uninstall of the Codex, Grok and Kimi blocks goes through the new
cbm_toml_remove_managed_block_owned with the header each block declares:
it removes our table with its keys and sub-tables and leaves everything
else in place. cbm_toml_remove_managed_block keeps the historical
whole-span contract.
Content whose ownership cannot be decided fails closed with the file
untouched: a second copy of a declared table, an undeclared extra
[[element]] of a declared array, a child of a declared array element, an
unparsable line in an owned table, a user key colliding with one the block
writes, a move that would hand the keys below the block to another table,
and a rewritten file whose tables conflict with the block.
Preserving was chosen over failing closed on every foreign table because
Codex keeps appending below a closing marker that ends the file. A
refusing installer would block every later install and uninstall until
the user hand-edits the TOML, and a hand edit is itself the likeliest way
to lose those tables. Moving whole sections keeps every byte and every
key's table, and the shapes that cannot be attributed still refuse.
Without foreign content the output is byte-identical to the old rewrite.
Fixes#2228
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
The cache directory holds two internal SQLite stores next to the project
indexes: the user's settings (_config.db) and the cross-repo store
(_cross_repo.db). cbm_list_indexes, cbm_remove_indexes and
count_db_indexes matched every "*.db" there. As a result:
- install --reset-indexes and uninstall (when index deletion is confirmed)
deleted the user's config (every `config set` value silently reverted
to its default) and the cross-repo store along with the indexes;
- the "Found N index(es)" listing and count over-reported by up to two.
pass_cross_repo.c already excluded both stores by exact filename, but in
its own copy of the check. Centralise the rule in foundation/str_util:
cbm_is_internal_cache_db() (exact names, so a real project whose name
starts with "_" or contains "config" is still an index) and
cbm_is_project_index_db(). Every enumeration of the cache directory's
.db files (list, count, remove, cross-repo target scan) now calls it, and
cbm_config_open() builds its path from the same CBM_CONFIG_DB_FILENAME
constant.
Proof on a real isolated cache (one indexed Go repo, `config set
auto_index true`, a _cross_repo.db present):
before: "Found 3 index(es)", "Removed 3 index(es)", cache left empty,
`config get auto_index` -> false
after: "Found 1 index(es)", "Removed 1 index(es)", _config.db and
_cross_repo.db kept, `config get auto_index` -> true
Test: cli::cli_index_enumeration_skips_internal_cache_dbs (RED on main,
green with the fix, RED again on revert).
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Upgrading from v0.10.8 to v0.11.0 on a machine with OpenCode reported all
three OpenCode subagent profiles as "preserved modified profile" plus an
op=agent_install error each, and the activation stopped ("one or more agent
configurations failed; the published/current executable was kept"), although
nobody had edited those files.
Root cause: #1933 (v0.11.0) added the tool_search / tool_search_regex
permissions to the rendered OpenCode profile. Install and uninstall recognise
a profile as ours only when it matches the current rendering or one of the
known released renderings (the other access mode, the v0.9.1-rc.1 Codex
shape, the pre-tier Verify file). The v0.10.8 OpenCode shape was not in that
set, so cbm_text_migrate_owned_document classified the untouched v0.10.8
files as user-modified. Reproduced end to end: install with the v0.10.8
release binary, then install with v0.11.0/main, into an isolated HOME; the
three profiles are 1729/1880/1910 bytes, the same sizes as in the report.
cbm_render_graph_profile_opencode_v0108() renders the pre-#1933 shape
(both access modes), and install/uninstall now list it as a released
rendering, so those files are upgraded in place and uninstall removes them
as owned. A profile the user actually edited is still preserved. The
released-list assembly that install and uninstall duplicated moves into one
helper, and the two legacy renderers share one implementation (cli.c drops
three raw free sites; the memory-core baseline is tightened 173 -> 170).
The Codex and OpenCode op=mcp_install errors in the same report do not
reproduce from a pristine v0.10.8 config and depend on the reporter's own
config.toml / opencode.json; they are not addressed here.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
`install` on a Hermes Agent config wrote the mcp_servers entry and the skill,
then failed op=pre_llm_hook_install on the same config.yaml. The stock Hermes
config (cli-config.yaml.example) reproduces it on its own.
Root cause: the nested-sequence editor behind the hooks.pre_llm_call item
validated EVERY line of the document and refused any flow collection or block
scalar anywhere. The stock config carries flow sequences in sections the hook
edit never reads or rewrites (`platform_toolsets:` -> `cli: [hermes-cli]`,
reporters' `plugins:` -> `enabled: [...]`). The mapping-entry editor that
writes mcp_servers into the same file already treats other top-level sections
as opaque user content, which is why that op succeeded.
Fix: yaml_sequence_validate_document now validates only the top-level section
the edit descends into (the first sequence_path key). The root mapping is
still validated at parse time, so section boundaries stay sound. An absent
section is appended as a new top-level key and touches no existing line.
Inside the edited `hooks` subtree the fail-closed rules are unchanged. This
also unblocks uninstall (op=pre_llm_hook_uninstall), which shares the analyzer.
Tests: new config_yaml_edit case with foreign flow sequences plus `|`/`>`
block scalars (install, byte-idempotent reinstall, remove). The two #1924
"still refuses" pins now place the unsupported construct inside `hooks:`,
where the refusal still applies byte-identically.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
On a machine whose profile path contains a space (C:\Users\First Last),
every install failed Codex with
op=hook_preflight reason=command_render
before config.toml was even read. The hook commands are rendered by
cbm_shell_quote_word / cbm_powershell_quote_word, which always single-quote
the installed binary path and accept a space (they refuse only control
bytes). The Codex hook block then validates its own rendered commands with
toml_codex_executable_is_safe, which refused every byte below 0x21 even
inside the single quotes. The validator was one character stricter than
the writer, so cbm refused the command it had just rendered, and the whole
activation stopped.
Inside the single-quoted form a space is literal in sh and PowerShell alike,
so the quoted branch now accepts 0x20. An unquoted executable word must
still be free of spaces (the shell would split it), and control bytes, DEL
and the unquoted metacharacters stay refused. The same check reads existing
hook entries back as owned, so a block written for a spaced path is adopted
on the next install and removed cleanly on uninstall.
Reproduced end to end with HOME containing a space on macOS, on v0.10.8 and
on main: install exited 1 with the exact error from the report. With the
fix it exits 0, writes both hook commands with the quoted path, a second
install is idempotent, and uninstall restores config.toml byte for byte.
Test: config_toml_codex_accepts_quoted_binary_path_with_spaces renders the
exact strings the two quoters emit for a spaced path (POSIX and Windows
forms) through check-only, upsert, idempotent re-upsert, and remove, and
pins that an unquoted spaced word is still refused with command_render.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Markdown docs reference other repo files constantly (a coding-standards
doc links the modules it governs, a README points at entry points) but
none of that surfaced as edges, so fan-in queries were blind to
documentation hubs. In an A/B retrieval benchmark I ran in August on a
docs-heavy repo, the graph's top fan-in answer was off by roughly 17x:
the most-referenced file was a standards doc with 173 references and
zero inbound edges.
New pre-dump pass, pass_doclinks.c, modeled on pass_configlink.c: three
strategies emit REFERENCES_FILE edges between existing File nodes only
(unresolvable targets are dropped, the pass never invents nodes):
inline links, backtick paths, bare path mentions. Targets resolve
against the referencing file's directory and the repo root; repeated
references collapse into one edge carrying strategy, confidence and
count. Registered in the pre-dump sequence after configlink and in the
incremental post-passes; REFERENCES_FILE added to the skill's edge-type
list and the structural/language contract tests.
Tests mirror test_configlink.c (real files in a tmpdir, File nodes in a
gbuf, run the pass, assert edges): inline link, backtick, bare mention,
http/anchor ignored, anchor-suffixed file link, dedupe with count,
relative-vs-root resolution, unresolvable-target guard, NULL repo_path
skip.
A companion change adds the same linking for shell files (source lines
and script invocations); split out to keep each change reviewable.
Validation: scripts/build.sh clean; focused serial runner (doclinks,
configlink, pipeline, edge_structural, lang_contract) 340 passed under
ASan/UBSan; cppcheck clean on the new files with the repo's flags.
Signed-off-by: Clément Deust <clement.deust@gmail.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
CLI_USAGE described outer --json but did not mention tool-level
--format json. Add a help-only pointer that tools which accept format
support --format tree|json, and distinguish payload JSON from the full
MCP envelope. No new flags, env vars, or output-default changes.
Fixes#2102
Signed-off-by: Lowpower <3133734+Lowpower@users.noreply.github.com>
Martin Vogel