@lzehrung/codegraph 2.1.1 → 2.2.0

package/README.md

@@ -18,7 +18,7 @@ codegraph is a local CLI **and TypeScript library** that turns a source tree int
 
 Without structural context, an agent burns early turns listing directories, guessing search terms, opening candidate files, and reconstructing relationships. codegraph does that discovery once so the context window can stay focused on the problem.
 
-On this repository under Node 24 with a warm cache, `codegraph orient --root . --budget small --json` returned in about **0.6s**, and the matching MCP `orient` call returned in about **100ms**.
+Warm-cache timings for `codegraph orient --root . --budget small --json` on this repository have ranged from about **0.6s** (Windows 11, Node 24) to about **2.5s** (a 4-core Linux container, Node 22), so treat them as machine-dependent rather than a headline figure; the matching MCP `orient` call returned in about **100ms** on the faster of the two. [The performance program index](docs/plans/2026-07-25-performance-program-index.md) records the current measurements and the conditions behind them.
 
 With Node.js 22.16 or newer, install from npm:
 
@@ -302,7 +302,7 @@ codegraph skill install --agent claude
 codegraph skill install --agent cursor
 ```
 
-See [Agent workflows](./docs/agent-workflows.md) for exploration strategy, warm sessions, streaming, review loops, and tool wrappers. See [MCP](./docs/mcp.md) for server and client configuration.
+See [Agent workflows](./docs/agent-workflows.md) for exploration strategy, warm sessions, streaming, review loops, and tool wrappers. Use `codegraph server start --root . --warmup` to share one local MCP HTTP server, then inspect or stop it with `codegraph server status --root . --json` and `codegraph server stop --root .`; lifecycle verification keeps its secret outside the project. See [MCP](./docs/mcp.md) for server and client configuration.
 
 ## Language support
 

package/codegraph-skill/codegraph/SKILL.md

@@ -20,6 +20,10 @@ Use plain text search for exact strings, logs, config keys, secrets, and prose.
 
 Bare `codegraph` prints five task-first routes without scanning the project. Use `codegraph --help` for the full command catalog and `codegraph help <command>` for command help; unknown commands suggest but never execute alternatives.
 
+Exit `0` means completion without a failure condition. Exit `1` can mean findings, no matching target, or a runtime failure. Inspect its output before continuing; findings and no matching targets are actionable, while runtime or analysis failures need error handling.
+
+Exit `2` means invalid usage or input. `links` uses `1` for broken local links; do not treat it as an invocation error.
+
 | Task                                                      | Start here                                               |
 | --------------------------------------------------------- | -------------------------------------------------------- |
 | Review staged and unstaged work                           | `codegraph review`                                       |
@@ -56,8 +60,9 @@ Use `--root` to define the boundary for config lookup, path confinement, and out
 
 `explore` returns ranked anchors, bounded packets, dependency paths, blast radius, candidate tests, explicit limits, omission counts, and copyable follow-ups. Human-readable output ends with `Recommended next:` using the first bounded follow-up; JSON keeps the stable `schemaVersion: 1` fields and `followUps` array as tool-call descriptors (`{tool, arguments, label?}`), not CLI strings. Hybrid search is code-first by default, and search, explain, explore, and review preserve analysis labels so reduced or mixed runs remain visible.
 
-Use `symbols` instead of hybrid `search` when only declarations should compete. It supports `--kind <kind,...>`, `--exported`, `--include-imports`, project-relative `--file-glob`, and `--limit <0-500>`; imports default off, and only named/default aliases that resolve to concrete declarations are returned.
+Use `search --no-snippets` when handles and paths are sufficient and source text will be fetched separately with `file`. Use `explain --changed-context` for bounded source context around changed ranges in changed-file or review workflows.
 
+Use `symbols` instead of hybrid `search` when only declarations should compete. It supports `--kind <kind,...>`, `--exported`, `--include-imports`, project-relative `--file-glob`, and `--limit <0-500>`; imports default off, and only named/default aliases that resolve to concrete declarations are returned.
 Use the portable callable handle from `symbols` with `codegraph callers <handle>` or `codegraph callees <handle>`. Depth defaults to 1 and caps at 5, the symbol limit defaults to 100 and caps at 500, pretty grouped callsites are the default, and `--json` returns the structured envelope.
 
 Call hierarchy contains resolved semantic `calls` edges only. `--include-heuristic` is accepted but currently adds no guessed dynamic calls; use `refs` for all references and `deps` or `rdeps` for file relationships.
@@ -85,10 +90,7 @@ The independent `--max-references`, `--max-callers`, and `--max-hierarchy` bound
 - references for every definition in a file: `codegraph refs <file>`
 
 Use line and column coordinates when known; this is the primary navigation form. Use an exact project-relative `file::symbol` path when coordinates are unavailable; it cannot be combined with line or column input. `deps` and `rdeps` accept either form or a portable `symbol:` handle and resolve it to its defining file, while `callers` and `callees` expose symbol-level calls. Duplicate local names return declaration candidates; run `codegraph symbols` to get a portable handle.
-
-### Review and Inspect
-
-Safe shorthand: `impact` and git-backed `drift` default to `HEAD..WORKTREE`; `artifact`, `packet`, and `mcp` infer `build`, `get`, and `serve`. `grep <regex>` and `sql <db> "SELECT ..."` accept positional forms. Explicit options remain valid. `grep --json` returns an envelope `{ items, limit, totalSeen, truncated, omitted }`, not a bare hit array: `limit` is the effective `--max-hits` cap for text greps (default 5000, capped at 200000) and `null` for uncapped `--query` AST greps. Check `truncated` before treating text results as complete, and raise `--max-hits` when it is true - `truncated` stays exact through that ceiling. `graph-delta --json` emits structured edge add/remove reports for revision ranges.
+Safe shorthand: `impact` and git-backed `drift` default to `HEAD..WORKTREE`; `artifact`, `packet`, and `mcp` infer `build`, `get`, and `serve`. `artifact --sqlite` is equivalent to `artifact build --sqlite`; `grep <regex>` and `sql <db> "SELECT ..."` accept positional forms. Explicit options remain valid. `grep --json` returns an envelope `{ items, limit, totalSeen, truncated, omitted }`, not a bare hit array: `limit` is the effective `--max-hits` cap for text greps (default 5000, capped at 200000) and `null` for uncapped `--query` AST greps. Check `truncated` before treating text results as complete, and raise `--max-hits` when it is true - `truncated` stays exact through that ceiling. `graph` output selectors are mutually exclusive.
 
 - compact review handoff: `codegraph review`
 - broader change impact: `codegraph impact --base HEAD --head WORKTREE`
@@ -100,6 +102,17 @@ Safe shorthand: `impact` and git-backed `drift` default to `HEAD..WORKTREE`; `ar
 - duplicate cleanup: `codegraph duplicates --root . ./src --profile cleanup`
 - full duplicate groups: `codegraph duplicates --root . ./src --json`
 - local Markdown link check: `codegraph links --json`
+- exported API summary: `codegraph apisurface --root . --json`
+- embedding-ready file chunks: `codegraph chunk src/auth.ts --json`
+- one indexed module: `codegraph dumpmod src/auth.ts --json`
+- prewarm or repair disk state: `codegraph index --root .`
+- inspect complex files: `codegraph hotspots --root . --limit 20`
+- list unresolved source imports: `codegraph unresolved --root . --json`
+- search text with a regex: `codegraph grep "TODO|FIXME" --glob "src/**/*.ts"`
+- query an exported SQLite graph: `codegraph sql codegraph.sqlite "SELECT * FROM files LIMIT 20"`
+- compare graph changes across revisions: `codegraph graph-delta --git-base origin/main --git-head HEAD --json`
+- create a durable artifact: `codegraph artifact --root . --out codegraph-out --sqlite --graph-json`
+- start a warm local tool server: `codegraph mcp --root . --stdio`
 
 `links` checks root-confined local Markdown links and GitHub-style heading fragments, including raw HTML `a[href]` in `.md` files. It skips external URLs and unsupported formats; exit 1 reports broken links. Discovery honors `codegraph.config.json` discovery globs plus CLI `--include-glob` / `--ignore-glob` / `--no-gitignore`. `review` and non-empty `impact` include the same `markdownLinks` findings; `unresolved` excludes document edges.
 
@@ -167,6 +180,8 @@ If MCP tools are available, prefer them over repeated CLI invocations. Use `expl
 codegraph uses the official MCP SDK v2 to serve current 2026-07-28 clients while retaining compatibility with 2025-era clients. MCP protocol connections and HTTP protocol sessions keep separate transport state, but all share the server's one warm codegraph analysis session for the configured root. Tool schemas reject unknown fields, each protocol session caps tool concurrency at 4 with a retryable busy error, HTTP request bodies time out after 30 seconds, and idle HTTP protocol sessions are evicted with a bounded session count. Cancellation responds to the caller promptly but retains the occupied slot until shared work settles, so abandoned calls cannot bypass that resource bound. Concurrent `refresh_index` calls serialize and honor each request's requested warmup.
 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 until the terminal result frame.
 HTTP enforces Host and Origin policies. A missing `Origin` is accepted for non-browser clients; unapproved, malformed, and opaque origins are rejected. This is not authentication: binding `--host` to a non-loopback address exposes an unauthenticated endpoint intended only for trusted networks or containers.
+For a reusable local HTTP server, run `codegraph server start --root . --warmup`, inspect it with `codegraph server status --root . --json`, and shut it down with `codegraph server stop --root .`. The lifecycle wrapper serializes project changes and writes `.codegraph/server.json` only after a challenged `/health` response proves the root, process, and startup time; its secret remains in the per-user Codegraph state directory, outside the project and separate from package files and compiler cache data. It defaults to `127.0.0.1:7331`, accepts `--startup-timeout-ms <1-86400000>` for warmups longer than 15 seconds, and writes startup diagnostics to `.codegraph/server.log`; add `--json` for `status: "started"`, registry fields, and update state.
+For stdio lifecycle control, pass `--idle-timeout-ms <milliseconds>`; `0` disables the timer and the option is rejected with HTTP `--port` transport.
 
 Use `refactor_plan` with flat `handle`, optional `renameTo`, independent optional `maxReferences`, `maxCallers`, and `maxHierarchy` bounds from 0 to 500, and optional `includeSource`. It reuses the configured server root and one session snapshot, returns portable targets and structured tool-call follow-ups even for exact internal review handles, exposes unsupported implementation sections in `sectionIssues`, preserves nested `rename.safe`, and never writes.
 Use `workspace_symbols` for deterministic symbol identities and exact ranges; use `search` when paths, prose, SQL, snippets, or graph evidence should participate.
@@ -199,15 +214,18 @@ codegraph install --target codex,claude --yes
 codegraph install --target codex --yes --force
 codegraph install --all --dry-run
 codegraph install --all --yes
+codegraph uninstall --target codex --yes
 ```
 
+Use `codegraph version` to inspect package identity and `codegraph skill doctor` to inspect bundled skill targets.
+
 Interactive confirmation accepts only `y` or `yes` and defaults to no. Noninteractive writes require `--yes`. `--all` is install-only, configures `codex`, `claude`, `cursor`, `gemini`, `opencode`, `omp`, `kilo`, and `agents`, and cannot be combined with target selection, `--detect`, or `--print-config`.
 
 Compatible JSON MCP entries and equivalent unmarked Codex tables are preserved byte-for-byte. Kilo JSONC comments and unrelated settings remain intact. Divergent codegraph entries are collision-reported without exposing configuration values.
 
 The installer manages codegraph-owned MCP entries, skill payloads, and marker files; uninstall removes only recognized codegraph-owned content. Existing user-owned `SKILL.md` files are preserved unless an ownership marker and known payload match, or `--force` is passed.
 
-Lifecycle commands manage `.codegraph/manifest.json`; other commands do not require that manifest:
+Lifecycle commands manage `.codegraph/manifest.json`; shared server commands separately manage `.codegraph/server.json` and `.codegraph/server.log`, and other commands do not require the manifest:
 
 ```bash
 codegraph init --root .
@@ -221,7 +239,7 @@ codegraph sync --root . --init --no-update-gitignore
 
 `init` and `sync --init` use Git's effective ignore semantics before lifecycle hashing. When the untracked manifest is not already ignored, they append exactly `.codegraph/` to the resolved root's `.gitignore`; effective parent/global/info excludes are honored, tracked manifests are left unchanged with a warning, and non-Git roots are not modified.
 
-Use `--no-update-gitignore` to opt out during `init` or `sync --init`; ordinary `sync` never updates ignore policy. `uninit` removes lifecycle state but leaves the root rule, while `init` and `sync` may warm or update `.codegraph-cache/index-v1/`.
+Use `--no-update-gitignore` to opt out during `init` or `sync --init`; ordinary `sync` never updates ignore policy. `uninit` preserves `.codegraph/server.json` and `.codegraph/server.log` even with `--force`, so stop a shared server explicitly; it leaves the root rule, while `init` and `sync` may warm or update `.codegraph-cache/index-v1/`.
 
 Lifecycle commands accept either one positional project path or `--root <path>`, never both. Automatic ignore updates are bound to that same resolved project root.
 

package/dist/agent/artifact.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"artifact.d.ts","sourceRoot":"","sources":["../../src/agent/artifact.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,KAAK,UAAU,EAAmB,MAAM,2BAA2B,CAAC;AAE7E,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAOxD,OAAO,KAAK,EAAE,oBAAoB,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAGvE,MAAM,MAAM,6BAA6B,GAAG;IAC1C,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,YAAY,CAAC;IAC5B,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,4BAA4B,GAAG;IACzC,aAAa,EAAE,CAAC,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE;QACT,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,SAAS,CAAC,EAAE,MAAM,CAAC;KACpB,CAAC;CACH,CAAC;AAqBF,KAAK,iBAAiB,GAAG;IACvB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,SAAS,EAAE,KAAK,CAAC;QACf,IAAI,EAAE,MAAM,CAAC;QACb,EAAE,EAAE;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,IAAI,EAAE,MAAM,CAAA;SAAE,GAAG;YAAE,IAAI,EAAE,UAAU,CAAC;YAAC,IAAI,EAAE,MAAM,CAAA;SAAE,CAAC;QACxE,GAAG,EAAE,MAAM,CAAC;QACZ,QAAQ,CAAC,EAAE,OAAO,CAAC;QACnB,QAAQ,CAAC,EAAE,WAAW,GAAG,SAAS,CAAC;QACnC,UAAU,CAAC,EAAE,MAAM,CAAC;KACrB,CAAC,CAAC;IACH,OAAO,EAAE,KAAK,CAAC,UAAU,GAAG;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC9C,WAAW,EAAE,oBAAoB,CAAC,aAAa,CAAC,CAAC,OAAO,CAAC,CAAC;CAC3D,CAAC;AAEF,KAAK,iBAAiB,GAAG,iBAAiB,GAAG;IAC3C,aAAa,EAAE,CAAC,CAAC;IACjB,MAAM,EAAE,sBAAsB,CAAC;IAC/B,KAAK,EAAE,iBAAiB,CAAC;CAC1B,CAAC;AAUF,wBAAsB,sBAAsB,CAC1C,OAAO,EAAE,6BAA6B,GACrC,OAAO,CAAC,4BAA4B,CAAC,CAWvC;AAED,wBAAsB,iCAAiC,CACrD,OAAO,EAAE,YAAY,EACrB,OAAO,EAAE,6BAA6B,GACrC,OAAO,CAAC,4BAA4B,CAAC,CAqFvC;AA6OD,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,oBAAoB,GAAG;IACvE,aAAa,EAAE,CAAC,CAAC;IACjB,MAAM,EAAE,sBAAsB,CAAC;IAC/B,KAAK,EAAE,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAClC,SAAS,EAAE,iBAAiB,CAAC,WAAW,CAAC,CAAC;IAC1C,OAAO,EAAE,iBAAiB,CAAC,SAAS,CAAC,CAAC;IACtC,WAAW,EAAE,iBAAiB,CAAC,aAAa,CAAC,CAAC;IAC9C,KAAK,EAAE,iBAAiB,CAAC,OAAO,CAAC,CAAC;CACnC,CAgFA"}

package/dist/agent/artifact.js

@@ -36,29 +36,35 @@ export async function buildCodegraphArtifactWithSession(session, request) {
     const selected = normalizeArtifactSelection(request);
     const filterOutDir = path.resolve(root, request.filterOutDir ?? request.outDir ?? DEFAULT_OUT_DIR);
     const snapshot = await filterSnapshotForOutputDirectory(await session.loadProject(), filterOutDir);
-    await fs.mkdir(outDir, { recursive: true });
-    if (request.force) {
-        await prepareForcedOutputDirectory(outDir, selected);
-    }
-    const artifacts = {};
+    const sqliteSignatures = [];
+    let sqliteFileSignatures = { signed: 0, skipped: 0 };
     if (selected.sqlite) {
-        if (!snapshot.fileSignatures) {
+        const snapshotFileSignatures = snapshot.fileSignatures;
+        if (!snapshotFileSignatures) {
             throw new Error("SQLite artifact freshness signatures are unavailable.");
         }
-        const fileSignatures = [];
         for (const file of snapshot.fileGraph.nodes) {
-            const signature = snapshot.fileSignatures.get(file);
+            const signature = snapshotFileSignatures.get(file);
             if (!signature) {
-                throw new Error(`SQLite artifact freshness signature is missing for ${file}.`);
+                sqliteFileSignatures = { ...sqliteFileSignatures, skipped: sqliteFileSignatures.skipped + 1 };
+                continue;
             }
-            fileSignatures.push({ path: signature.file, size: signature.size, mtimeMs: signature.mtimeMs });
+            sqliteSignatures.push({ path: signature.file, size: signature.size, mtimeMs: signature.mtimeMs });
         }
+        sqliteFileSignatures = { signed: sqliteSignatures.length, skipped: sqliteFileSignatures.skipped };
+    }
+    await fs.mkdir(outDir, { recursive: true });
+    if (request.force) {
+        await prepareForcedOutputDirectory(outDir, selected);
+    }
+    const artifacts = {};
+    if (selected.sqlite) {
         const outputPath = path.join(outDir, SQLITE_FILE);
         await writeGraphSqlite({
             fileGraph: snapshot.fileGraph,
             symbolGraph: snapshot.symbolGraph,
             outputPath,
-            fileSignatures,
+            fileSignatures: sqliteSignatures,
         });
         artifacts.sqlite = SQLITE_FILE;
     }
@@ -91,6 +97,7 @@ export async function buildCodegraphArtifactWithSession(session, request) {
         sql: {
             supported: true,
             limitation: "SQL support does not perform current-schema reconstruction.",
+            fileSignatures: sqliteFileSignatures,
         },
         graphJsonSchema: "codegraph.graph-json",
     };
@@ -209,6 +216,8 @@ async function readCodegraphManifest(outDir) {
         if (key === "questions")
             artifacts.questions = artifactFile;
     }
+    const sql = isPlainRecord(value.sql) ? value.sql : undefined;
+    const fileSignatures = sql && isPlainRecord(sql.fileSignatures) ? sql.fileSignatures : undefined;
     return {
         schemaVersion: 1,
         root: typeof value.root === "string" ? value.root : "",
@@ -218,6 +227,10 @@ async function readCodegraphManifest(outDir) {
         sql: {
             supported: true,
             limitation: "",
+            fileSignatures: {
+                signed: typeof fileSignatures?.signed === "number" ? fileSignatures.signed : 0,
+                skipped: typeof fileSignatures?.skipped === "number" ? fileSignatures.skipped : 0,
+            },
         },
         graphJsonSchema: "codegraph.graph-json",
     };
@@ -316,6 +329,7 @@ function outputIgnoreGlobs(root, outDir) {
 }
 export function buildCodegraphGraphJson(snapshot) {
     const symbolIds = buildPortableSymbolIdMap(snapshot);
+    const symbolPositions = buildPortableSymbolPositions(snapshot, symbolIds);
     const portableSymbolId = (id) => symbolIds.get(id) ?? id;
     const graph = {
         files: [...snapshot.fileGraph.nodes].map((file) => normalizeAgentFilePath(snapshot.root, file)).sort(),
@@ -331,9 +345,26 @@ export function buildCodegraphGraphJson(snapshot) {
             const fromDelta = left.from.localeCompare(right.from);
             if (fromDelta !== 0)
                 return fromDelta;
+            const leftToType = left.to.type;
+            const rightToType = right.to.type;
+            const toTypeDelta = leftToType.localeCompare(rightToType);
+            if (toTypeDelta !== 0)
+                return toTypeDelta;
             const leftTo = left.to.type === "file" ? left.to.path : left.to.name;
             const rightTo = right.to.type === "file" ? right.to.path : right.to.name;
-            return leftTo.localeCompare(rightTo);
+            const toDelta = leftTo.localeCompare(rightTo);
+            if (toDelta !== 0)
+                return toDelta;
+            const rawDelta = left.raw.localeCompare(right.raw);
+            if (rawDelta !== 0)
+                return rawDelta;
+            const typeOnlyDelta = Number(left.typeOnly ?? false) - Number(right.typeOnly ?? false);
+            if (typeOnlyDelta !== 0)
+                return typeOnlyDelta;
+            const resolvedDelta = (left.resolved ?? "").localeCompare(right.resolved ?? "");
+            if (resolvedDelta !== 0)
+                return resolvedDelta;
+            return (left.confidence ?? -1) - (right.confidence ?? -1);
         }),
         symbols: [...snapshot.symbolGraph.nodes.values()]
             .map((node) => ({
@@ -345,7 +376,21 @@ export function buildCodegraphGraphJson(snapshot) {
             const fileDelta = left.file.localeCompare(right.file);
             if (fileDelta !== 0)
                 return fileDelta;
-            return left.name.localeCompare(right.name);
+            const nameDelta = left.name.localeCompare(right.name);
+            if (nameDelta !== 0)
+                return nameDelta;
+            const kindDelta = left.kind.localeCompare(right.kind);
+            if (kindDelta !== 0)
+                return kindDelta;
+            const leftPosition = symbolPositions.get(left.id) ?? ZERO_SYMBOL_POSITION;
+            const rightPosition = symbolPositions.get(right.id) ?? ZERO_SYMBOL_POSITION;
+            const lineDelta = leftPosition.line - rightPosition.line;
+            if (lineDelta !== 0)
+                return lineDelta;
+            const columnDelta = leftPosition.column - rightPosition.column;
+            if (columnDelta !== 0)
+                return columnDelta;
+            return left.id.localeCompare(right.id);
         }),
         symbolEdges: [...snapshot.symbolGraph.edges]
             .map((edge) => ({
@@ -360,7 +405,10 @@ export function buildCodegraphGraphJson(snapshot) {
             const toDelta = left.to.localeCompare(right.to);
             if (toDelta !== 0)
                 return toDelta;
-            return (left.label ?? "").localeCompare(right.label ?? "");
+            const labelDelta = (left.label ?? "").localeCompare(right.label ?? "");
+            if (labelDelta !== 0)
+                return labelDelta;
+            return compareSymbolEdgeSites(snapshot.root, left.site, right.site);
         }),
     };
     return {
@@ -373,6 +421,49 @@ export function buildCodegraphGraphJson(snapshot) {
         graph,
     };
 }
+const ZERO_SYMBOL_POSITION = { line: 0, column: 0 };
+function buildPortableSymbolPositions(snapshot, symbolIds) {
+    const positions = new Map();
+    for (const moduleIndex of snapshot.index.byFile.values()) {
+        for (const local of moduleIndex.locals) {
+            const portableId = symbolIds.get(defNodeId(local));
+            if (!portableId)
+                continue;
+            positions.set(portableId, {
+                line: local.range.start.line,
+                column: local.range.start.column,
+            });
+        }
+    }
+    return positions;
+}
+function compareSymbolEdgeSites(root, left, right) {
+    if (!left && !right)
+        return 0;
+    if (!left)
+        return -1;
+    if (!right)
+        return 1;
+    const fileDelta = normalizeAgentFilePath(root, left.file).localeCompare(normalizeAgentFilePath(root, right.file));
+    if (fileDelta !== 0)
+        return fileDelta;
+    const startLineDelta = left.range.start.line - right.range.start.line;
+    if (startLineDelta !== 0)
+        return startLineDelta;
+    const startColumnDelta = left.range.start.column - right.range.start.column;
+    if (startColumnDelta !== 0)
+        return startColumnDelta;
+    const startIndexDelta = (left.range.start.index ?? -1) - (right.range.start.index ?? -1);
+    if (startIndexDelta !== 0)
+        return startIndexDelta;
+    const endLineDelta = left.range.end.line - right.range.end.line;
+    if (endLineDelta !== 0)
+        return endLineDelta;
+    const endColumnDelta = left.range.end.column - right.range.end.column;
+    if (endColumnDelta !== 0)
+        return endColumnDelta;
+    return (left.range.end.index ?? -1) - (right.range.end.index ?? -1);
+}
 function buildPortableSymbolIdMap(snapshot) {
     const byId = new Map();
     const graphNodeIds = new Set();

package/dist/agent/artifact.js.map

@@ -1 +1 @@
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package/dist/agent/explain.d.ts

@@ -128,6 +128,9 @@ export type AgentExplanation = {
         duplicates: number;
         snippets: number;
     };
+    omittedCountsLowerBounds: {
+        references: boolean;
+    };
     changedContext?: AgentExplanationChangedContext;
 };
 export declare function explainCodegraphTarget(request: AgentExplainTarget): Promise<AgentExplanation>;

package/dist/agent/explain.d.ts.map

@@ -1 +1 @@
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package/dist/agent/explain.js

@@ -259,6 +259,9 @@ async function buildExplanation(snapshot, lookup, resolved, request) {
             duplicates: duplicates.omitted,
             snippets: snippets.omitted,
         },
+        omittedCountsLowerBounds: {
+            references: referenceContext.referencesOmittedLowerBound,
+        },
         ...(changedContext ? { changedContext } : {}),
     };
 }
@@ -295,6 +298,9 @@ function emptyExplanation(snapshot, target) {
             duplicates: 0,
             snippets: 0,
         },
+        omittedCountsLowerBounds: {
+            references: false,
+        },
     };
 }
 function explainTarget(snapshot, resolved, relFile) {
@@ -481,6 +487,7 @@ async function collectReferenceContext(snapshot, def, referenceLimit, snippetLim
     return {
         references: boundedReferences,
         snippets: boundedSnippets,
+        referencesOmittedLowerBound: result.references.length === collectionLimit && boundedReferences.omitted > 0,
     };
 }
 function snippetFromReference(snapshot, reference) {
@@ -644,6 +651,7 @@ function emptyReferenceContext() {
     return {
         references: emptyAgentBoundedList(),
         snippets: emptyAgentBoundedList(),
+        referencesOmittedLowerBound: false,
     };
 }
 function collectFollowUps(snapshot, resolved, symbols, relFile, duplicates) {