npm - @lzehrung/codegraph - Versions diffs - 3.1.0 → 3.1.1 - Mend

@lzehrung/codegraph 3.1.0 → 3.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (101) hide show

package/codegraph-skill/codegraph/SKILL.md +3 -2
package/dist/agent/explain.d.ts.map +1 -1
package/dist/agent/explain.js +12 -7
package/dist/agent/explain.js.map +1 -1
package/dist/agent/search.d.ts +13 -0
package/dist/agent/search.d.ts.map +1 -1
package/dist/agent/search.js +10 -4
package/dist/agent/search.js.map +1 -1
package/dist/bin/cli.js +1644 -675
package/dist/cli/command-table.d.ts.map +1 -1
package/dist/cli/command-table.js +4 -0
package/dist/cli/command-table.js.map +1 -1
package/dist/cli/duplicates.d.ts +5 -0
package/dist/cli/duplicates.d.ts.map +1 -1
package/dist/cli/duplicates.js +15 -2
package/dist/cli/duplicates.js.map +1 -1
package/dist/cli/help.d.ts +4 -4
package/dist/cli/help.d.ts.map +1 -1
package/dist/cli/help.js +15 -9
package/dist/cli/help.js.map +1 -1
package/dist/cli/mcp.d.ts.map +1 -1
package/dist/cli/mcp.js +4 -0
package/dist/cli/mcp.js.map +1 -1
package/dist/cli/options.d.ts.map +1 -1
package/dist/cli/options.js +5 -1
package/dist/cli/options.js.map +1 -1
package/dist/cli/progress.d.ts.map +1 -1
package/dist/cli/progress.js +42 -16
package/dist/cli/progress.js.map +1 -1
package/dist/cli/server.d.ts.map +1 -1
package/dist/cli/server.js +2 -0
package/dist/cli/server.js.map +1 -1
package/dist/cli/viewer.js +1 -1
package/dist/cli/viewer.js.map +1 -1
package/dist/drift/git.d.ts.map +1 -1
package/dist/drift/git.js +10 -2
package/dist/drift/git.js.map +1 -1
package/dist/duplicates/candidates.d.ts +61 -0
package/dist/duplicates/candidates.d.ts.map +1 -0
package/dist/duplicates/candidates.js +873 -0
package/dist/duplicates/candidates.js.map +1 -0
package/dist/duplicates/progress.d.ts +17 -0
package/dist/duplicates/progress.d.ts.map +1 -0
package/dist/duplicates/progress.js +57 -0
package/dist/duplicates/progress.js.map +1 -0
package/dist/duplicates/scoring.d.ts +9 -40
package/dist/duplicates/scoring.d.ts.map +1 -1
package/dist/duplicates/scoring.js +34 -414
package/dist/duplicates/scoring.js.map +1 -1
package/dist/duplicates/types.d.ts +30 -1
package/dist/duplicates/types.d.ts.map +1 -1
package/dist/duplicates/units.d.ts +2 -1
package/dist/duplicates/units.d.ts.map +1 -1
package/dist/duplicates/units.js +24 -3
package/dist/duplicates/units.js.map +1 -1
package/dist/duplicates.d.ts +1 -0
package/dist/duplicates.d.ts.map +1 -1
package/dist/duplicates.js +116 -62
package/dist/duplicates.js.map +1 -1
package/dist/impact/providers/base.js +1 -1
package/dist/impact/providers/base.js.map +1 -1
package/dist/mcp/cancellation.d.ts +6 -0
package/dist/mcp/cancellation.d.ts.map +1 -0
package/dist/mcp/cancellation.js +11 -0
package/dist/mcp/cancellation.js.map +1 -0
package/dist/mcp/handlers.d.ts +33 -3
package/dist/mcp/handlers.d.ts.map +1 -1
package/dist/mcp/handlers.js +128 -30
package/dist/mcp/handlers.js.map +1 -1
package/dist/mcp/http-transport.d.ts.map +1 -1
package/dist/mcp/http-transport.js +7 -4
package/dist/mcp/http-transport.js.map +1 -1
package/dist/mcp/index-readiness.d.ts +114 -0
package/dist/mcp/index-readiness.d.ts.map +1 -0
package/dist/mcp/index-readiness.js +264 -0
package/dist/mcp/index-readiness.js.map +1 -0
package/dist/mcp/protocol.d.ts.map +1 -1
package/dist/mcp/protocol.js +23 -10
package/dist/mcp/protocol.js.map +1 -1
package/dist/mcp/server.d.ts +2 -0
package/dist/mcp/server.d.ts.map +1 -1
package/dist/mcp/server.js +9 -4
package/dist/mcp/server.js.map +1 -1
package/dist/mcp/stale-install.d.ts +13 -0
package/dist/mcp/stale-install.d.ts.map +1 -0
package/dist/mcp/stale-install.js +30 -0
package/dist/mcp/stale-install.js.map +1 -0
package/dist/review/deleted.js +1 -1
package/dist/review/deleted.js.map +1 -1
package/dist/review.d.ts +6 -0
package/dist/review.d.ts.map +1 -1
package/dist/review.js +1 -1
package/dist/review.js.map +1 -1
package/dist/types.d.ts +2 -0
package/dist/types.d.ts.map +1 -1
package/dist/util/concurrency.d.ts +7 -0
package/dist/util/concurrency.d.ts.map +1 -1
package/dist/util/concurrency.js +11 -0
package/dist/util/concurrency.js.map +1 -1
package/docs/mcp.md +56 -7
package/package.json +3 -3

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package/dist/review.d.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 import { type DuplicatePreparedAnalysis } from "./duplicates.js";
 import { type ProjectIndex } from "./indexer/types.js";
+import { type ReviewChangeCollection } from "./review/changes.js";
 import type { ReviewOptions, ReviewReport } from "./review/types.js";
 export type { ReviewBuildReport, ReviewChangedFileSummaries, ReviewDepth, ReviewDiagnostics, ReviewFileSummary, ReviewOptions, ReviewReport, ReviewRiskLevel, ReviewRiskSummary, ReviewSymbolCallsite, ReviewSymbolSummary, ReviewTask, ReviewTaskPriority, ReviewTimingReport, } from "./review/types.js";
 /**
@@ -15,5 +16,10 @@ export declare function buildReviewReport(projectRoot: string, opts?: ReviewOpti
     loadIndex?: () => Promise<ProjectIndex>;
     duplicateAnalysis?: DuplicatePreparedAnalysis;
     loadDuplicateAnalysis?: () => Promise<DuplicatePreparedAnalysis>;
+    /**
+     * @internal The changes that `collectReviewChanges` returned for these same options, from a caller that already
+     * asked git for them. The report uses them instead of collecting again, and records no timings for collecting.
+     */
+    changes?: ReviewChangeCollection;
 }): Promise<ReviewReport>;
 //# sourceMappingURL=review.d.ts.map

package/dist/review.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"review.d.ts","sourceRoot":"","sources":["../src/review.ts"],"names":[],"mappings":"AAEA,OAAO,EAIL,KAAK,yBAAyB,EAE/B,MAAM,iBAAiB,CAAC;AAIzB,OAAO,EAAE,KAAK,YAAY,EAAkB,MAAM,oBAAoB,CAAC;AAQvE,OAAO,EAA+C,KAAK,sBAAsB,EAAE,MAAM,qBAAqB,CAAC;AAU/G,OAAO,KAAK,EAKV,aAAa,EACb,YAAY,EAGb,MAAM,mBAAmB,CAAC;AAE3B,YAAY,EACV,iBAAiB,EACjB,0BAA0B,EAC1B,WAAW,EACX,iBAAiB,EACjB,iBAAiB,EACjB,aAAa,EACb,YAAY,EACZ,eAAe,EACf,iBAAiB,EACjB,oBAAoB,EACpB,mBAAmB,EACnB,UAAU,EACV,kBAAkB,EAClB,kBAAkB,GACnB,MAAM,mBAAmB,CAAC;AA4J3B;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,MAAM,EACnB,IAAI,GAAE,aAAkB,EACxB,MAAM,CAAC,EAAE;IACP,KAAK,CAAC,EAAE,YAAY,CAAC;IACrB,SAAS,CAAC,EAAE,MAAM,OAAO,CAAC,YAAY,CAAC,CAAC;IACxC,iBAAiB,CAAC,EAAE,yBAAyB,CAAC;IAC9C,qBAAqB,CAAC,EAAE,MAAM,OAAO,CAAC,yBAAyB,CAAC,CAAC;IACjE;;;OAGG;IACH,OAAO,CAAC,EAAE,sBAAsB,CAAC;CAClC,GACA,OAAO,CAAC,YAAY,CAAC,CAkKvB"}

package/dist/review.js CHANGED Viewed

@@ -131,7 +131,7 @@ export async function buildReviewReport(projectRoot, opts = {}, cached) {
         delete reviewReport.duplicateAnalysis;
     }
     const totalStart = performance.now();
-    const { changedFiles, explicitFiles, diffHunksByFile, diffKindsByFile, diffChangesByFile } = await collectReviewChanges(projectRoot, appliedOptions, reviewTimings);
+    const { changedFiles, explicitFiles, diffHunksByFile, diffKindsByFile, diffChangesByFile } = cached?.changes ?? (await collectReviewChanges(projectRoot, appliedOptions, reviewTimings));
     if (changedFiles.size === 0) {
         const riskSummary = computeRiskSummary({
             filesChanged: 0,

package/dist/review.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/types.d.ts CHANGED Viewed

@@ -35,6 +35,8 @@ export type ProgressUpdate = {
     activity?: string;
     current: number;
     total: number;
+    /** Singular noun the count measures (`unit`, `pair`). The display pluralizes it. Defaults to `file`. */
+    unit?: string;
     phase?: "start" | "update" | "complete";
     mode?: "build" | "update" | "check";
     elapsedMs?: number;

package/dist/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/util/concurrency.d.ts CHANGED Viewed

@@ -25,4 +25,11 @@ export declare function mapLimitSemaphore<T, R>(items: T[], limit: number, fn: (
 export declare function getIOSemaphore(limit?: number): Semaphore;
 export declare function resetIOSemaphore(): void;
 export declare function delay(ms: number): Promise<void>;
+/** How long a loop on the main thread may run before it lets timers and I/O callbacks that are due have a turn. */
+export declare const EVENT_LOOP_SLICE_MS = 10;
+/**
+ * Lets the timers and I/O callbacks that are due run. Awaiting a promise that is already settled does not: a loop that
+ * awaits only such promises keeps the event loop from every timer until it ends.
+ */
+export declare function yieldToEventLoop(): Promise<void>;
 //# sourceMappingURL=concurrency.d.ts.map

package/dist/util/concurrency.d.ts.map CHANGED Viewed

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package/dist/util/concurrency.js CHANGED Viewed

@@ -130,4 +130,15 @@ export function delay(ms) {
     setTimeout(resolve, ms);
     return promise;
 }
+/** How long a loop on the main thread may run before it lets timers and I/O callbacks that are due have a turn. */
+export const EVENT_LOOP_SLICE_MS = 10;
+/**
+ * Lets the timers and I/O callbacks that are due run. Awaiting a promise that is already settled does not: a loop that
+ * awaits only such promises keeps the event loop from every timer until it ends.
+ */
+export function yieldToEventLoop() {
+    const { promise, resolve } = Promise.withResolvers();
+    setImmediate(resolve);
+    return promise;
+}
 //# sourceMappingURL=concurrency.js.map

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	@@ -1 +1 @@
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package/docs/mcp.md CHANGED Viewed

@@ -20,7 +20,7 @@ codegraph server status --root /path/to/repo --json
 codegraph server stop --root /path/to/repo
 ```
-`server start` serializes lifecycle changes, launches `mcp serve`, waits for a same-root process and startup identity proved by a challenged `/health` response, then records the process at `.codegraph/server.json`. It defaults to `127.0.0.1:7331`; use `--host` explicitly for a non-loopback bind, `--replace` only to restart a live server for the same root, and `--startup-timeout-ms <1-86400000>` when a warmup needs more than the 15-second default.
+`server start` serializes lifecycle changes, launches `mcp serve`, waits for a same-root process and startup identity proved by a challenged `/health` response, then records the process at `.codegraph/server.json`. It defaults to `127.0.0.1:7331`; use `--host` explicitly for a non-loopback bind, `--replace` only to restart a live server for the same root, and `--startup-timeout-ms <1-86400000>` when the process needs more than the 15-second default to start answering `/health`. The index warmup runs in the background after that and does not count against the timeout.
 `server start --json` emits `status: "started"`, the registry fields, and `update`. `server status` retries challenged HTTP health checks and reports a verification remedy instead of removing metadata for an unreachable or identity-mismatched server. `server stop` removes only confirmed stale metadata or signals a Codegraph process whose proven health identity matches the registry.
@@ -32,14 +32,14 @@ Use `mcp serve` directly when another process manager owns the server:
 codegraph mcp serve --root /path/to/repo --port 7331
 ```
-Startup warms the base session cache by default now, matching the commands above. Pass `--no-warmup` for the old lazy startup, or `--warmup-symbols` to also build the detailed symbol graph before serving:
+The server answers `initialize` and `tools/list` as soon as it is serving, then builds the base session cache and the search index in the background (the default, `--warmup`). Pass `--warmup-symbols` to also build the detailed symbol graph in the background, or `--no-warmup` to build nothing up front:
 ```bash
 codegraph mcp serve --root . --stdio --no-warmup
 codegraph mcp serve --root . --port 7331 --warmup-symbols
 ```
-`--warmup` builds the base session cache before serving requests (the default). `--warmup-symbols` also builds the detailed symbol graph before serving requests. `--no-warmup` skips both and starts lazily.
+With `--no-warmup`, the first tool call that needs the index starts the build. In every mode, `search`, `explore`, `orient`, `get_file` with `includeGraphContext`, `review`, `packet_get`, `workspace_symbols`, and `impact` wait for a running build for at most `--index-wait-ms` (default 15000) and then answer `index_building`; every other tool waits for the index without a limit. See [Cold start and `index_building`](#cold-start-and-index_building).
 The server also watches the project for file changes and refreshes the index in the background. Pass `--no-watch` to turn that off; see [File watcher](#file-watcher).
@@ -51,7 +51,9 @@ HTTP protocol sessions track last activity, cap concurrent legacy sessions (defa
 Each MCP server permits four concurrent tool calls by default across every HTTP request and protocol session; a saturated server returns a retryable busy error rather than queueing unbounded work. The programmatic server options `mcpToolConcurrency`, `httpBodyTimeoutMs`, and `mcpToolTimeoutMs` tune concurrency, the 30-second HTTP request-body deadline, and the 5-minute per-tool execution deadline; an HTTP body that misses its deadline receives `408 Request Timeout`, while an expired tool call is aborted and names its configured limit. Completed legacy requests refresh session activity before idle eviction is considered.
-Client cancellation returns promptly, but does not discard shared index or artifact work. A cancelled call continues to occupy its concurrency slot until its underlying operation settles, preventing a burst of abandoned requests from exceeding the configured resource bound; the MCP SDK aborts the individual in-flight HTTP request when its response socket closes without closing the shared protocol session. Shutdown rejects new calls and waits for active work before invalidating shared session resources.
+`mcpIndexWaitMs` (CLI `--index-wait-ms`) bounds only the wait of those tools for an index build, not the tool call itself; see [Cold start and `index_building`](#cold-start-and-index_building).
+Client cancellation returns promptly, but does not discard shared index or artifact work. A cancelled call continues to occupy its concurrency slot until its underlying operation settles, preventing a burst of abandoned requests from exceeding the configured resource bound; the MCP SDK aborts the individual in-flight HTTP request when its response socket closes without closing the shared protocol session. Shutdown rejects new calls and waits for active work, for the startup warmup, and for every index load that a call started, including one whose call stopped waiting or failed, before invalidating shared session resources.
 Use stdio for a client-owned subprocess. Use HTTP for one long-running codegraph process per repository, then point every MCP-capable IDE, terminal, or agent client at the same local URL. Exact config keys vary by client, but the MCP settings should use HTTP/Streamable HTTP transport plus the `/mcp` URL instead of a `command`/`args` stdio launch.
@@ -69,6 +71,8 @@ On Windows, installed-package servers map the verified native addon from `%LOCAL
 The published CLI and MCP runtime is a self-contained bundle rather than a set of lazy content-hashed chunks. This prevents an in-place package upgrade from deleting code that an already running server has not loaded yet; restart the client after an upgrade to select the new runtime.
+A server that keeps running through an upgrade can still need a module that the upgrade removed. The tool call then returns `isError: true` with a message that the codegraph package changed on disk and the MCP server must be restarted, in place of Node's `Cannot find module` text.
 Run `codegraph doctor` in the installed release to inspect `native.origin`, `native.update`, and any stale npm retirement siblings. `updateSafeForCurrentProcess` describes only the process running doctor; it does not prove that no other process or filesystem service holds a package file.
 ## Tools
@@ -115,10 +119,10 @@ For MCP `explore`, `includeSource` defaults to `false`: source-bearing packets d
 ## Session lifecycle
-MCP keeps one codegraph session warm for the configured root. That makes follow-up calls cheaper than separate CLI invocations. `mcp serve` warms the base session cache during startup by default (matching the old `--warmup` flag), so a cold discovery-and-build cost lands on process startup rather than the first `tools/call`. Pass `--no-warmup` to start lazily instead, or `--warmup-symbols` to also build the detailed symbol graph before serving.
+MCP keeps one codegraph session warm for the configured root. That makes follow-up calls cheaper than separate CLI invocations. `mcp serve` builds the base session cache and the search index in the background once it is serving, so a cold discovery-and-build cost no longer delays `initialize` or `tools/list`. Pass `--no-warmup` to build only when a tool call needs the index, or `--warmup-symbols` to also build the detailed symbol graph.
 On the first `tools/call`, codegraph can emit `notifications/message` and, when the request includes `_meta.progressToken`, `notifications/progress` before the final result. Stdio carries them inline, and modern Streamable HTTP clients that accept `text/event-stream` receive them as a stream.
-Because startup now warms by default, a client's startup/readiness timeout - not just its per-request timeout - needs to cover a cold build on a large repository; the `startup_timeout_ms = 20000` Codex example below can be too short for a first run against a large tree. Raise `startup_timeout_ms` for large repositories, or pass `--no-warmup` to keep process startup instant and shift that cost back to the first `tools/call` (clients that enforce per-request timeouts should then send `_meta.progressToken` so they can keep a slow first request alive instead of timing it out).
+The `startup_timeout_ms = 20000` Codex example below is enough for a large repository: the server answers `initialize` at once and no longer builds before it serves. A client's per-request timeout is what a cold build can exceed, and [Cold start and `index_building`](#cold-start-and-index_building) keeps each request inside it.
 Text and hybrid searches reuse a prepared handle for `.codegraph/cache/index-v1/search-v1.sqlite` and cache identical responses by snapshot identity and request options. A detected refresh or explicit `refresh_index` closes the handle and clears cached responses before the next snapshot.
@@ -129,6 +133,49 @@ A session created with `freshness: { policy: "manual" }` (only possible when a l
 `get_file` reads live bytes from disk after path confinement. It does not require a fresh index; only an explicit `includeGraphContext: true` checks indexed freshness and adds direct graph context, so returned file bytes and `totalLines` remain live even when `freshness` reports stale context.
 Tool schemas are flat JSON objects for broad client compatibility; argument combinations such as `refs` handle-vs-position mode are validated by the server. Legacy paired names (`callers`, `callees`, `supertypes`, `subtypes`, `deps`, and `rdeps`) remain accepted by `tools/call` as aliases, but only the unified tools appear in `tools/list`.
+### Cold start and `index_building`
+The first run on a large project builds the index from scratch, which can take longer than the 30 seconds that MCP clients commonly allow for one request. The main read tools stay inside that window:
+- `initialize` and `tools/list` answer at once on stdio and HTTP. The warmup starts after the server is serving and runs in the background; the HTTP server listens before it ends.
+- `search`, `explore`, `orient`, `get_file` with `includeGraphContext`, `review`, `packet_get`, `workspace_symbols`, and `impact` wait for the builds they read for at most `--index-wait-ms` (default 15000). The warmup and concurrent calls share each build, so a call joins one that is running instead of starting another.
+- Every other tool, such as `goto`, `refs`, `calls`, `file_deps`, `query_sqlite`, `refresh_index`, and `artifact_build`, waits for the index without a limit, as it did before. A client that calls one of them during a cold build needs a request timeout that covers the build.
+- `get_file` without `includeGraphContext` never waits: it reads the file from disk under the same root confinement as always. A `review` of a range without a changed file is answered from git and waits for nothing.
+When one of these tools waits at all, it first waits for a build that is running, because it checks freshness against it, then for what it reads:
+| Tool                | Reads                                                                                                                                                                                   |
+| ------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `search`            | The project index. `hybrid`, `symbol`, and `graph` also read the symbol graph, and `hybrid` and `text` the search index. A `path` search without `from` lists files and reads no index. |
+| `explore`           | What a `hybrid` `search` reads. With `includeSource` (off by default over MCP) and `maxPackets` above 0, also the detailed symbol graph and the duplicate analysis.                     |
+| `orient`            | The project index.                                                                                                                                                                      |
+| `workspace_symbols` | The project index.                                                                                                                                                                      |
+| `impact`            | The project index.                                                                                                                                                                      |
+| `get_file`          | The project index, only with `includeGraphContext`.                                                                                                                                     |
+| `review`            | The project index and the duplicate analysis, for a range with a changed file.                                                                                                          |
+| `packet_get`        | The detailed symbol graph, and for a file or symbol target the duplicate analysis (a SQL object or an unresolved target needs none). A `review:` target reads no session build.         |
+A call of these tools that has waited `--index-wait-ms` without its builds ending returns a normal result, not an error, and the builds continue:
+```json
+{
+  "status": "index_building",
+  "tool": "search",
+  "message": "Codegraph is still building the index for this project (Building search index, 19s so far). The build continues in the background; call 'search' again to wait for it.",
+  "retryAfterMs": 1000,
+  "waitedMs": 15003,
+  "progress": { "activity": "Building search index", "elapsedMs": 19100 }
+}
+```
+- Call the same tool again. The retry joins the builds that run, waits for what is left of them, up to the same budget, and then returns the normal result.
+- `progress.activity` names what is running, such as `Indexing files` or `Preparing duplicate analysis`. `current` and `total` appear only while the work has a measurable total, such as files parsed.
+- A cancelled request stops waiting at once; the builds are not cancelled.
+- When the session is replaced while a call waits, because a file changed, the file watcher refreshed, or `refresh_index` ran, the call builds what it reads again inside the same budget, up to three times in all.
+- The budget is a timer on the server's event loop. The builds hand the loop back every few milliseconds, between files, so the answer normally arrives within a second or two of the budget. A single large file can hold the loop longer, and a call also runs its own work once its builds end (a `review` of a large diff, for example), so keep the budget at least ten seconds below the client's timeout.
+Choose a request timeout longer than `--index-wait-ms`: the default of 15 seconds leaves a client that allows 30 fifteen seconds for the work that follows the builds; for a project where that is not enough, lower the budget. For a client that allows less, lower the budget (`--index-wait-ms 8000`); for one that allows more, raise it, or pass `--index-wait-ms 0` to make these tools wait for as long as the builds take too (the per-tool deadline still applies). Library callers set `mcpIndexWaitMs`. The setting belongs to the server: `codegraph.config.json` has no key for it.
 ### File watcher
 `mcp serve` and `server start` watch the project root while the server runs, unless you pass `--no-watch`. The watcher is a hint: the freshness check that every index-backed tool call runs stays the authority, so a missed event costs speed, never correctness.
@@ -137,7 +184,7 @@ Tool schemas are flat JSON objects for broad client compatibility; argument comb
 - 500 ms after the last event, and at least 5 seconds after the previous background refresh ended, the server runs the freshness check and rebuilds the index in the background. Each new event restarts the 500 ms wait, so no refresh starts while events still arrive. A query that arrives during the rebuild waits for it, as on a cold start.
 - The background rebuild also covers a change burst above the automatic refresh limits (50 files or 2 MB, for example a branch switch), which a query alone reports as `stale` until `refresh_index`. A session that cannot read its configuration keeps its snapshot, as it does without the watcher.
 - One refresh runs at a time, and events during it schedule exactly one more. A refresh takes its turn in the same queue as `refresh_index`, `artifact_build`, and the automatic SQLite artifact refresh, so `refresh_index` waits for a rebuild that is running instead of starting a second one beside it. A refresh that still waits for its turn when a newer event arrives, or when the watcher pauses, gives the turn up: the burst that the event belongs to starts its own refresh once it settles. On Linux, each read of the file list for the per-directory watches takes its turn in that queue as well, so the first read of a server that started with `--no-warmup` cannot overlap a `refresh_index`. A failed refresh writes `[codegraph] watch refresh failed: <message>` to stderr and leaves the freshness check as it was.
-- When the server shuts down (stdin closes, or the HTTP server closes), it stops the watches and timers at once, then waits for a refresh that is running and for a read of the file list that has started before it releases the session, so that neither writes the cache or the file signatures afterwards.
+- When the server shuts down (stdin closes, or the HTTP server closes), it stops the watches and timers at once, then waits for a refresh that is running, for a read of the file list that has started, for the startup warmup, and for every index load that the warmup or a call started, including one whose call stopped waiting and one that ran beside a load that failed, before it releases the session, so that none writes the cache or the file signatures afterwards.
 - After 30 minutes without a tool call, the server closes every watch and cancels pending refreshes, including one that still waits for its turn behind a `refresh_index` or an `artifact_build`. The next tool call reopens the watches and clears the cached freshness result first, so the check sees every edit made during the pause. This matters most for `codegraph server start`, whose process lives until `server stop`.
 - Windows and macOS use one recursive watch on the root. Other platforms use one watch per directory that holds a discovered file, because Node's recursive watching on Linux walks the whole tree, `node_modules` included, and can exhaust inotify watches.
 - A watch that is lost with its directory (a deleted project root on Windows, a removed and recreated directory on Linux) closes at the first event that names the directory and counts as a change; the next refresh opens it again once the directory exists.
@@ -212,6 +259,8 @@ Only resolved, indexed `extends` and `implements` relationships are returned. Im
 Call `get_file` with a project-relative `file`. `offset` is the 1-based first line, `limit` is the maximum returned lines, and `maxBytes` bounds unnumbered raw page text including its line separators; defaults are `1`, `2000`, and `80000`, with output-page caps of `10000` lines and `500000` bytes. A separate 16 MiB hard input-size limit rejects larger raw reads and structural text-config summaries before unbounded I/O, bounding complete-stream binary/UTF-8 validation and total-line counting rather than returned page size.
+`file` is required and must be a project-relative path string. A missing, `null`, or non-string value is rejected with JSON-RPC `-32602` and `Invalid parameters for get_file: file: expected a project-relative file path string, received null`.
 ```json
 {
   "file": "src/auth.ts",

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@lzehrung/codegraph",
-  "version": "3.1.0",
+  "version": "3.1.1",
   "type": "module",
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",
@@ -82,8 +82,8 @@
   "license": "MIT",
   "description": "Multi-language repository map for agents and humans: MCP tools, dependency graphs, symbol indexes, impact review, and bounded source evidence.",
   "dependencies": {
-    "@lzehrung/codegraph-core": "3.1.0",
-    "@lzehrung/codegraph-native": "^2.1.0",
+    "@lzehrung/codegraph-core": "3.1.1",
+    "@lzehrung/codegraph-native": "^2.1.1",
     "@modelcontextprotocol/node": "^2.1.1",
     "@modelcontextprotocol/server": "^2.3.1",
     "jsonc-parser": "^3.3.1",