codesift-mcp 0.5.21 → 0.5.27

package/dist/tools/graph-tools.js

@@ -15,41 +15,68 @@ const CALLABLE_KINDS = new Set([
 ]);
 /**
  * Extract identifiers that look like function/method calls from source code.
- * Matches patterns like: `functionName(`, `obj.methodName(`, `this.method(`
- * Also matches JSX component usage: `<ComponentName`, which captures React
- * component rendering as a call-graph edge (PascalCase filter skips HTML tags).
- * Returns a Set of the called/used identifier names.
+ * Matches patterns like: `functionName(`, `obj.methodName(`, `this.method(`.
+ * Also matches JSX component usage: `<ComponentName`.
+ *
+ * Returns an array of CallSite entries with an `is_method_call` flag so
+ * downstream graph consumers can exclude method calls from bare-function
+ * caller edges (root cause fix for builtin hub contamination, spec D4).
+ *
+ * Method-call detection: the match position is preceded by `.` or `?.`
+ * (including surrounding whitespace). Bracket notation `obj["map"]()` is
+ * NOT detected (documented residual noise per spec).
  */
 function extractCallSites(source) {
-    const calls = new Set();
+    const calls = [];
+    const seen = new Set();
+    function push(name, is_method_call) {
+        const key = `${name}\0${is_method_call ? "1" : "0"}`;
+        if (seen.has(key))
+            return;
+        seen.add(key);
+        calls.push({ name, is_method_call });
+    }
+    // Method-call detection — look back one or two chars for `.` or `?.`
+    function isMethodCallAt(index) {
+        let i = index - 1;
+        // skip whitespace between dot and identifier (rare but valid: `obj . map(`)
+        while (i >= 0 && (source[i] === " " || source[i] === "\t"))
+            i--;
+        if (i < 0)
+            return false;
+        if (source[i] === ".") {
+            // `?.map(` — optional chaining
+            if (i - 1 >= 0 && source[i - 1] === "?")
+                return true;
+            return true;
+        }
+        return false;
+    }
     // Match: word followed by ( — captures function calls and method calls
     // Also handles: this.method(, obj.method(, await func(, new Class(
     const callPattern = /\b([a-zA-Z_$][\w$]*)\s*(?:<[^>]*>)?\s*\(/g;
     let match;
     while ((match = callPattern.exec(source)) !== null) {
         const name = match[1];
-        // Skip language keywords that look like calls
-        if (!KEYWORD_SET.has(name) && name.length >= MIN_CALL_NAME_LENGTH) {
-            calls.add(name);
-        }
+        if (KEYWORD_SET.has(name) || name.length < MIN_CALL_NAME_LENGTH)
+            continue;
+        push(name, isMethodCallAt(match.index));
     }
     // JSX component usage: <PascalCaseComponent ...> or <PascalCaseComponent/>
-    // PascalCase filter (<[A-Z]) skips HTML elements like <div>, <span>, <button>.
-    // This makes trace_call_chain, impact_analysis, find_dead_code etc. React-aware.
     const jsxPattern = /<([A-Z][a-zA-Z0-9_$]*)\b/g;
     while ((match = jsxPattern.exec(source)) !== null) {
         const name = match[1];
         if (name.length >= MIN_CALL_NAME_LENGTH) {
-            calls.add(name);
+            push(name, false);
         }
     }
     // PHP method and static calls: ->method(, ::method(
-    // e.g. $this->render(, Yii::$app->db->createCommand(, User::find(
     const phpCallPattern = /(?:->|::)([a-zA-Z_][\w]*)\s*\(/g;
     while ((match = phpCallPattern.exec(source)) !== null) {
         const name = match[1];
         if (!KEYWORD_SET.has(name) && name.length >= MIN_CALL_NAME_LENGTH) {
-            calls.add(name);
+            // -> and :: are accessor operators — these are method/static calls
+            push(name, true);
         }
     }
     return calls;
@@ -113,7 +140,15 @@ function buildAdjacencyIndex(allSymbols, skipTests = true, filterReactHooks = fa
             continue;
         const callSites = extractCallSites(sym.source);
         const symCallees = [];
-        for (const calledName of callSites) {
+        for (const site of callSites) {
+            // Root-cause fix for builtin hub contamination (D4 Layer 1):
+            // `arr.map(...)` is a method call on the receiver's type, not a
+            // call to a bare function named `map`. Drop method calls from
+            // caller-edge construction so `map`/`filter`/`slice`/etc defined
+            // locally don't accumulate fake callers.
+            if (site.is_method_call)
+                continue;
+            const calledName = site.name;
             // Filter out React stdlib hooks when requested (reduces graph noise)
             if (filterReactHooks && REACT_STDLIB_HOOKS.has(calledName))
                 continue;
@@ -338,9 +373,14 @@ export async function findCircularDeps(repo, options) {
     if (!index)
         throw new Error(`Repository "${repo}" not found`);
     const edges = await collectImportEdges(index);
+    // Exclude type-only edges from cycle detection. `edge.type_only === true` is
+    // explicit type-only (Python TYPE_CHECKING / TS `import type`); `undefined`
+    // and `false` continue to participate so JS/JSX/PHP cycle detection works
+    // and TS-AST-failure regex-fallback edges are still considered.
+    const runtimeEdges = edges.filter((e) => e.type_only !== true);
     const filteredEdges = options?.file_pattern
-        ? edges.filter((e) => e.from.includes(options.file_pattern) || e.to.includes(options.file_pattern))
-        : edges;
+        ? runtimeEdges.filter((e) => e.from.includes(options.file_pattern) || e.to.includes(options.file_pattern))
+        : runtimeEdges;
     // Build directed adjacency (from → to only)
     const adj = new Map();
     for (const edge of filteredEdges) {
@@ -386,11 +426,94 @@ export async function findCircularDeps(repo, options) {
             dfs(node);
         }
     }
-    return {
+    const result = {
         cycles,
         total_files: new Set([...filteredEdges.map((e) => e.from), ...filteredEdges.map((e) => e.to)]).size,
         total_edges: filteredEdges.length,
     };
+    // Package-level cycles (Task 12) — only when index.workspaces is populated.
+    if (index.workspaces && index.workspaces.length > 0) {
+        const pkg = computePackageLevelCycles(index.workspaces);
+        if (pkg.package_cycles.length > 0)
+            result.package_cycles = pkg.package_cycles;
+        if (pkg.unresolved.length > 0)
+            result.unresolved_workspace_refs = pkg.unresolved;
+    }
+    return result;
+}
+/** Compute package-level cycles in a JS/TS monorepo workspace graph.
+ *  Filters unresolved dependencies before SCC to avoid crashes (gemini fix
+ *  in plan rev 5). Cycles are returned as arrays of workspace names; each
+ *  closed cycle includes the wrap-around (e.g. ["a", "b", "a"]).
+ *  Limitation: DFS-with-color guarantees finding at least one elementary
+ *  cycle per strongly-connected component but does NOT enumerate all of
+ *  them. Sufficient for monorepo scale (<100 packages). */
+function computePackageLevelCycles(workspaces) {
+    const knownNames = new Set();
+    for (const ws of workspaces) {
+        if (ws.name)
+            knownNames.add(ws.name);
+    }
+    const adj = new Map();
+    const unresolved = [];
+    for (const ws of workspaces) {
+        if (!ws.name)
+            continue;
+        const filtered = [];
+        for (const dep of ws.dependencies.workspace) {
+            if (knownNames.has(dep)) {
+                filtered.push(dep);
+            }
+            else {
+                unresolved.push({ from_workspace: ws.name, missing_dep: dep });
+            }
+        }
+        if (filtered.length > 0)
+            adj.set(ws.name, filtered);
+    }
+    // DFS-based cycle detection on the cleaned graph (mirrors file-level pattern)
+    const visited = new Set();
+    const inStack = new Set();
+    const stack = [];
+    const cycleSignatures = new Set();
+    const package_cycles = [];
+    function dfs(node) {
+        if (inStack.has(node)) {
+            const idx = stack.indexOf(node);
+            if (idx >= 0) {
+                const cycle = [...stack.slice(idx), node];
+                // Canonicalize so [a,b,a] and [b,a,b] dedupe to one entry
+                const signature = canonicalCycleSignature(cycle.slice(0, -1));
+                if (!cycleSignatures.has(signature)) {
+                    cycleSignatures.add(signature);
+                    package_cycles.push({ cycle, length: cycle.length - 1 });
+                }
+            }
+            return;
+        }
+        if (visited.has(node))
+            return;
+        visited.add(node);
+        inStack.add(node);
+        stack.push(node);
+        for (const next of adj.get(node) ?? [])
+            dfs(next);
+        stack.pop();
+        inStack.delete(node);
+    }
+    for (const node of adj.keys())
+        dfs(node);
+    return { package_cycles, unresolved };
+}
+function canonicalCycleSignature(nodes) {
+    if (nodes.length === 0)
+        return "";
+    let minIdx = 0;
+    for (let i = 1; i < nodes.length; i++) {
+        if (nodes[i] < nodes[minIdx])
+            minIdx = i;
+    }
+    return [...nodes.slice(minIdx), ...nodes.slice(0, minIdx)].join(">");
 }
 // Export shared utilities for impact-tools and testing
 export { buildAdjacencyIndex, extractCallSites, buildCallTree, stripSource, isTestFile, classifyRole };

package/dist/tools/graph-tools.js.map

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package/dist/tools/hotspot-tools.d.ts

@@ -11,6 +11,12 @@ export interface HotspotResult {
     period: string;
     total_files: number;
     total_commits: number;
+    /**
+     * Diagnostic note populated only when the result is empty or degraded.
+     * Audit skills should surface this in their Tool Availability Block as
+     * `EMPTY-RESULT (<note>)` instead of silently treating it as "no hotspots".
+     */
+    note?: string;
 }
 /**
  * Analyze git churn hotspots: files with high change frequency × complexity.

package/dist/tools/hotspot-tools.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"hotspot-tools.d.ts","sourceRoot":"","sources":["../../src/tools/hotspot-tools.ts"],"names":[],"mappings":"AAMA,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,aAAa,EAAE,MAAM,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,WAAW,EAAE,CAAC;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;CACvB;AAmFD;;;GAGG;AACH,wBAAsB,eAAe,CACnC,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IACR,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAChC,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,YAAY,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACnC,GACA,OAAO,CAAC,aAAa,CAAC,CAkDxB"}
+{"version":3,"file":"hotspot-tools.d.ts","sourceRoot":"","sources":["../../src/tools/hotspot-tools.ts"],"names":[],"mappings":"AASA,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,aAAa,EAAE,MAAM,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,WAAW,EAAE,CAAC;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB;;;;OAIG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAuGD;;;GAGG;AACH,wBAAsB,eAAe,CACnC,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IACR,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAChC,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,YAAY,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACnC,GACA,OAAO,CAAC,aAAa,CAAC,CAoExB"}

package/dist/tools/hotspot-tools.js

@@ -1,26 +1,47 @@
-import { execFileSync } from "node:child_process";
+import { execFile } from "node:child_process";
+import { promisify } from "node:util";
 import { getCodeIndex } from "./index-tools.js";
+const execFileAsync = promisify(execFile);
 const DEFAULT_SINCE_DAYS = 90;
 const MAX_HOTSPOTS = 30;
 /**
  * Get git log numstat for a repo: file → { commits, linesChanged }.
+ *
+ * Async to avoid blocking the MCP server's event loop while git produces output.
+ * On a 2,376-commit repo with --numstat, the synchronous variant could block for
+ * tens of seconds, exceeding the MCP client's connection timeout (-32000).
+ *
+ * Returns a tuple of [churn-map, error-note]. error-note is populated when the
+ * git invocation failed or produced empty output — caller should surface it
+ * rather than treating empty as "no hotspots."
  */
-function getGitChurn(repoRoot, sinceDays) {
+async function getGitChurn(repoRoot, sinceDays, useAllRefs = false) {
     const since = `${sinceDays} days ago`;
+    const args = ["log", "--numstat", "--format=%H", `--since=${since}`];
+    if (useAllRefs)
+        args.push("--all");
     let output;
     try {
-        output = execFileSync("git", [
-            "log", "--numstat", "--format=%H", `--since=${since}`,
-        ], {
+        const result = await execFileAsync("git", args, {
             cwd: repoRoot,
             encoding: "utf-8",
             timeout: 30_000,
+            maxBuffer: 50 * 1024 * 1024, // 50MB — --numstat on 2k+ commit repos
         });
+        output = result.stdout;
     }
     catch (err) {
         const message = err instanceof Error ? err.message : String(err);
         console.error(`[hotspot] git log failed for ${repoRoot}: ${message}`);
-        return new Map();
+        return { churn: new Map(), note: `git log failed: ${message.slice(0, 200)}` };
+    }
+    if (!output.trim()) {
+        return {
+            churn: new Map(),
+            note: useAllRefs
+                ? `git log returned empty output even with --all refs (no commits in last ${sinceDays}d)`
+                : `git log returned empty output (no commits in last ${sinceDays}d on current ref)`,
+        };
     }
     const churn = new Map();
     const lines = output.split("\n");
@@ -72,7 +93,7 @@ function getGitChurn(repoRoot, sinceDays) {
         if (entry)
             entry.commits++;
     }
-    return churn;
+    return { churn };
 }
 /**
  * Analyze git churn hotspots: files with high change frequency × complexity.
@@ -86,7 +107,22 @@ export async function analyzeHotspots(repo, options) {
     const sinceDays = options?.since_days ?? DEFAULT_SINCE_DAYS;
     const topN = options?.top_n ?? MAX_HOTSPOTS;
     const filePattern = options?.file_pattern;
-    const churn = getGitChurn(index.root, sinceDays);
+    let { churn, note } = await getGitChurn(index.root, sinceDays);
+    // Empty-result fallback: structure-audit-2026-04-30 saw analyze_hotspots return
+    // empty on an active 2,376-commit repo. Cause was never identified (resolver
+    // bug + worktree state both possible). Try --all refs as a recovery before
+    // giving up — covers detached HEAD, unusual ref configs, and worktrees.
+    if (churn.size === 0 && !note?.includes("git log failed")) {
+        console.error(`[hotspot] empty churn for ${index.root} on default ref — retrying with --all`);
+        const fallback = await getGitChurn(index.root, sinceDays, /* useAllRefs */ true);
+        churn = fallback.churn;
+        if (churn.size > 0) {
+            note = `recovered via --all refs fallback (default ref returned empty)`;
+        }
+        else {
+            note = fallback.note ?? `empty churn even after --all fallback`;
+        }
+    }
     // Build symbol count lookup
     const symbolCounts = new Map();
     for (const file of index.files) {
@@ -94,7 +130,10 @@ export async function analyzeHotspots(repo, options) {
     }
     const hotspots = [];
     let totalCommits = 0;
+    let yieldCounter = 0;
     for (const [file, stats] of churn) {
+        if ((++yieldCounter & 511) === 0)
+            await new Promise((r) => setImmediate(r));
         if (filePattern && !file.includes(filePattern))
             continue;
         // Skip non-indexed files (node_modules, etc.)
@@ -119,6 +158,7 @@ export async function analyzeHotspots(repo, options) {
         period: `last ${sinceDays} days`,
         total_files: hotspots.length,
         total_commits: Math.round(totalCommits / Math.max(hotspots.length, 1)),
+        ...(note ? { note } : {}),
     };
 }
 //# sourceMappingURL=hotspot-tools.js.map

package/dist/tools/hotspot-tools.js.map

@@ -1 +1 @@
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package/dist/tools/impact-tools.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"impact-tools.d.ts","sourceRoot":"","sources":["../../src/tools/impact-tools.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAkD,YAAY,EAAE,MAAM,aAAa,CAAC;AAkHhG,MAAM,WAAW,aAAa;IAC5B,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,cAAc,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CACtC;AAED;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,cAAc,CAAC,EAAE,MAAM,GAAG,aAAa,EACvC,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,YAAY,CAAC,CAiEvB"}
+{"version":3,"file":"impact-tools.d.ts","sourceRoot":"","sources":["../../src/tools/impact-tools.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAkD,YAAY,EAAE,MAAM,aAAa,CAAC;AAkHhG,MAAM,WAAW,aAAa;IAC5B,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,cAAc,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CACtC;AAED;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,cAAc,CAAC,EAAE,MAAM,GAAG,aAAa,EACvC,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,YAAY,CAAC,CAwEvB"}

package/dist/tools/impact-tools.js

@@ -123,8 +123,15 @@ export async function impactAnalysis(repo, since, depthOrOptions, until) {
     // Find all symbols in changed files — use Set for O(1) lookup (CQ17 fix)
     const changedFileSet = new Set(changedFiles);
     const changedSymbols = index.symbols.filter((s) => changedFileSet.has(s.file));
-    // Build adjacency index once, reuse for both affected + dependency graph
-    // Include test files for impact analysis (want to know which tests are affected)
+    // Build adjacency index once, reuse for both affected + dependency graph.
+    // Include test files for impact analysis (want to know which tests are affected).
+    //
+    // Monorepo note (Task 14 of monorepo workspace intelligence plan):
+    // buildAdjacencyIndex resolves callers/callees by symbol name across the
+    // ENTIRE indexed symbol set, so cross-package symbol references propagate
+    // automatically when both packages live in the same CodeIndex. Workspace
+    // metadata on `index.workspaces` (Task 7) is therefore NOT consulted here —
+    // it is already implicit in the symbol set.
     const adjacency = buildAdjacencyIndex(index.symbols, false);
     const allAffected = findAffectedSymbols(changedSymbols, adjacency, maxDepth);
     // Cap affected symbols to prevent massive responses

package/dist/tools/impact-tools.js.map

@@ -1 +1 @@
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package/dist/tools/index-tools.d.ts

@@ -17,6 +17,12 @@ export declare function indexFolder(folderPath: string, options?: {
     incremental?: boolean | undefined;
     include_paths?: string[] | undefined;
     watch?: boolean | undefined;
+    /**
+     * Cap on files indexed in a single pass. When the walker hits this, it
+     * returns partial results with a warning rather than blowing through
+     * memory. Default: DEFAULT_MAX_FILES (or CODESIFT_MAX_FILES env var).
+     */
+    max_files?: number | undefined;
 }): Promise<IndexFolderResult>;
 /**
  * Clone a remote git repository and index it.
@@ -60,6 +66,12 @@ export declare function ensureIndexFresh(repoName: string): Promise<{
 }>;
 /** Reset freshness throttle cache. Exported for testing. */
 export declare function resetFreshnessCache(): void;
+/** Stop every active watcher and clear the in-memory index caches. Exported
+ *  for testing — afterAll teardown of integration tests that index temp dirs
+ *  must call this before `rm -rf`-ing the temp dir, otherwise the chokidar
+ *  watcher races the rm and emits ENOTEMPTY/ENOENT noise that shows up as
+ *  file-level test failures even when every test inside passed. */
+export declare function stopAllWatchersForTesting(): Promise<void>;
 /**
  * Get the in-memory BM25 index for a repo.
  * Loads from disk if not cached. Auto-refreshes if git HEAD moved.
@@ -72,7 +84,9 @@ export declare function getBM25Index(repoName: string): Promise<BM25Index | null
 /**
  * Get the code index for a repo from disk. Auto-refreshes if git HEAD moved.
  */
-export declare function getCodeIndex(repoName: string): Promise<CodeIndex | null>;
+export declare function getCodeIndex(repoName: string, options?: {
+    skipFreshness?: boolean;
+}): Promise<CodeIndex | null>;
 /**
  * Called at server startup. If the CWD is inside a git repo that isn't indexed yet,
  * index it automatically in the background so tools work without manual setup.

package/dist/tools/index-tools.d.ts.map

@@ -1 +1 @@
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