@colbymchenry/codegraph-darwin-arm64 0.9.3 → 0.9.5

package/lib/dist/graph/traversal.js

@@ -68,24 +68,22 @@ class GraphTraverser {
                 const priority = (e) => e.kind === 'contains' ? 0 : e.kind === 'calls' ? 1 : 2;
                 return priority(a) - priority(b);
             });
+            // Batch-fetch the unvisited neighbors in one query (was N+1 per BFS step).
+            const wantIds = adjacentEdges
+                .map((e) => (e.source === node.id ? e.target : e.source))
+                .filter((id) => !visited.has(id));
+            const neighborNodes = wantIds.length > 0 ? this.queries.getNodesByIds(wantIds) : new Map();
             for (const adjEdge of adjacentEdges) {
-                // Determine next node: for 'both' direction, edges can be either
-                // incoming or outgoing, so pick whichever end is not the current node
                 const nextNodeId = adjEdge.source === node.id ? adjEdge.target : adjEdge.source;
-                if (visited.has(nextNodeId)) {
+                if (visited.has(nextNodeId))
                     continue;
-                }
-                const nextNode = this.queries.getNodeById(nextNodeId);
-                if (!nextNode) {
+                const nextNode = neighborNodes.get(nextNodeId);
+                if (!nextNode)
                     continue;
-                }
-                // Apply node kind filter
                 if (opts.nodeKinds && opts.nodeKinds.length > 0 && !opts.nodeKinds.includes(nextNode.kind)) {
                     continue;
                 }
-                // Add node to result
                 nodes.set(nextNode.id, nextNode);
-                // Queue for further traversal
                 queue.push({ node: nextNode, edge: adjEdge, depth: depth + 1 });
             }
         }
@@ -131,17 +129,18 @@ class GraphTraverser {
         visited.add(node.id);
         // Get adjacent edges
         const adjacentEdges = this.getAdjacentEdges(node.id, opts.direction, opts.edgeKinds);
+        // Batch-fetch unvisited neighbors (was N+1 per DFS step).
+        const wantIds = adjacentEdges
+            .map((e) => (e.source === node.id ? e.target : e.source))
+            .filter((id) => !visited.has(id));
+        const neighborNodes = wantIds.length > 0 ? this.queries.getNodesByIds(wantIds) : new Map();
         for (const edge of adjacentEdges) {
-            // Determine next node: for 'both' direction, edges can be either
-            // incoming or outgoing, so pick whichever end is not the current node
             const nextNodeId = edge.source === node.id ? edge.target : edge.source;
-            if (visited.has(nextNodeId)) {
+            if (visited.has(nextNodeId))
                 continue;
-            }
-            const nextNode = this.queries.getNodeById(nextNodeId);
-            if (!nextNode) {
+            const nextNode = neighborNodes.get(nextNodeId);
+            if (!nextNode)
                 continue;
-            }
             // Apply node kind filter
             if (opts.nodeKinds && opts.nodeKinds.length > 0 && !opts.nodeKinds.includes(nextNode.kind)) {
                 continue;
@@ -190,8 +189,14 @@ class GraphTraverser {
         }
         visited.add(nodeId);
         const incomingEdges = this.queries.getIncomingEdges(nodeId, ['calls', 'references', 'imports']);
+        if (incomingEdges.length === 0)
+            return;
+        // Batch-fetch all caller nodes in one round-trip instead of one
+        // getNodeById per edge (was N+1 — meaningful on functions with many callers).
+        const sourceIds = incomingEdges.map((e) => e.source);
+        const callerNodes = this.queries.getNodesByIds(sourceIds);
         for (const edge of incomingEdges) {
-            const callerNode = this.queries.getNodeById(edge.source);
+            const callerNode = callerNodes.get(edge.source);
             if (callerNode && !visited.has(callerNode.id)) {
                 result.push({ node: callerNode, edge });
                 this.getCallersRecursive(callerNode.id, maxDepth, currentDepth + 1, result, visited);
@@ -217,8 +222,13 @@ class GraphTraverser {
         }
         visited.add(nodeId);
         const outgoingEdges = this.queries.getOutgoingEdges(nodeId, ['calls', 'references', 'imports']);
+        if (outgoingEdges.length === 0)
+            return;
+        // Batch-fetch callee nodes (was N+1 — see getCallersRecursive note).
+        const targetIds = outgoingEdges.map((e) => e.target);
+        const calleeNodes = this.queries.getNodesByIds(targetIds);
         for (const edge of outgoingEdges) {
-            const calleeNode = this.queries.getNodeById(edge.target);
+            const calleeNode = calleeNodes.get(edge.target);
             if (calleeNode && !visited.has(calleeNode.id)) {
                 result.push({ node: calleeNode, edge });
                 this.getCalleesRecursive(calleeNode.id, maxDepth, currentDepth + 1, result, visited);
@@ -291,8 +301,11 @@ class GraphTraverser {
         }
         visited.add(nodeId);
         const outgoingEdges = this.queries.getOutgoingEdges(nodeId, ['extends', 'implements']);
+        if (outgoingEdges.length === 0)
+            return;
+        const parents = this.queries.getNodesByIds(outgoingEdges.map((e) => e.target));
         for (const edge of outgoingEdges) {
-            const parentNode = this.queries.getNodeById(edge.target);
+            const parentNode = parents.get(edge.target);
             if (parentNode && !nodes.has(parentNode.id)) {
                 nodes.set(parentNode.id, parentNode);
                 edges.push(edge);
@@ -306,8 +319,11 @@ class GraphTraverser {
         }
         visited.add(nodeId);
         const incomingEdges = this.queries.getIncomingEdges(nodeId, ['extends', 'implements']);
+        if (incomingEdges.length === 0)
+            return;
+        const children = this.queries.getNodesByIds(incomingEdges.map((e) => e.source));
         for (const edge of incomingEdges) {
-            const childNode = this.queries.getNodeById(edge.source);
+            const childNode = children.get(edge.source);
             if (childNode && !nodes.has(childNode.id)) {
                 nodes.set(childNode.id, childNode);
                 edges.push(edge);
@@ -325,11 +341,14 @@ class GraphTraverser {
         const result = [];
         // Get all incoming edges (references, calls, type_of, etc.)
         const incomingEdges = this.queries.getIncomingEdges(nodeId);
+        if (incomingEdges.length === 0)
+            return result;
+        // Batch-fetch source nodes (was N+1).
+        const sources = this.queries.getNodesByIds(incomingEdges.map((e) => e.source));
         for (const edge of incomingEdges) {
-            const sourceNode = this.queries.getNodeById(edge.source);
-            if (sourceNode) {
+            const sourceNode = sources.get(edge.source);
+            if (sourceNode)
                 result.push({ node: sourceNode, edge });
-            }
         }
         return result;
     }
@@ -372,21 +391,27 @@ class GraphTraverser {
             const containerKinds = new Set(['class', 'interface', 'struct', 'trait', 'protocol', 'module', 'enum']);
             if (containerKinds.has(focalNode.kind)) {
                 const containsEdges = this.queries.getOutgoingEdges(nodeId, ['contains']);
-                for (const edge of containsEdges) {
-                    const childNode = this.queries.getNodeById(edge.target);
-                    if (childNode && !visited.has(childNode.id)) {
-                        nodes.set(childNode.id, childNode);
-                        edges.push(edge);
-                        // Recurse into children at the same depth (they're part of the same symbol)
-                        this.getImpactRecursive(childNode.id, maxDepth, currentDepth, nodes, edges, visited);
+                if (containsEdges.length > 0) {
+                    const children = this.queries.getNodesByIds(containsEdges.map((e) => e.target));
+                    for (const edge of containsEdges) {
+                        const childNode = children.get(edge.target);
+                        if (childNode && !visited.has(childNode.id)) {
+                            nodes.set(childNode.id, childNode);
+                            edges.push(edge);
+                            // Recurse into children at the same depth (they're part of the same symbol)
+                            this.getImpactRecursive(childNode.id, maxDepth, currentDepth, nodes, edges, visited);
+                        }
                     }
                 }
             }
         }
         // Get all incoming edges (things that depend on this node)
         const incomingEdges = this.queries.getIncomingEdges(nodeId);
+        if (incomingEdges.length === 0)
+            return;
+        const sources = this.queries.getNodesByIds(incomingEdges.map((e) => e.source));
         for (const edge of incomingEdges) {
-            const sourceNode = this.queries.getNodeById(edge.source);
+            const sourceNode = sources.get(edge.source);
             if (sourceNode && !nodes.has(sourceNode.id)) {
                 nodes.set(sourceNode.id, sourceNode);
                 edges.push(edge);
@@ -424,9 +449,16 @@ class GraphTraverser {
             visited.add(nodeId);
             // Get outgoing edges
             const outgoingEdges = this.queries.getOutgoingEdges(nodeId, edgeKinds.length > 0 ? edgeKinds : undefined);
+            if (outgoingEdges.length === 0)
+                continue;
+            // Batch-fetch only the unvisited targets (was N+1 per BFS frontier).
+            const wantIds = outgoingEdges
+                .map((e) => e.target)
+                .filter((id) => !visited.has(id));
+            const nextNodes = wantIds.length > 0 ? this.queries.getNodesByIds(wantIds) : new Map();
             for (const edge of outgoingEdges) {
                 if (!visited.has(edge.target)) {
-                    const nextNode = this.queries.getNodeById(edge.target);
+                    const nextNode = nextNodes.get(edge.target);
                     if (nextNode) {
                         queue.push({
                             nodeId: edge.target,
@@ -479,12 +511,15 @@ class GraphTraverser {
      */
     getChildren(nodeId) {
         const containsEdges = this.queries.getOutgoingEdges(nodeId, ['contains']);
+        if (containsEdges.length === 0)
+            return [];
+        // Batch-fetch (was N+1).
+        const childNodes = this.queries.getNodesByIds(containsEdges.map((e) => e.target));
         const children = [];
         for (const edge of containsEdges) {
-            const childNode = this.queries.getNodeById(edge.target);
-            if (childNode) {
+            const childNode = childNodes.get(edge.target);
+            if (childNode)
                 children.push(childNode);
-            }
         }
         return children;
     }

package/lib/dist/graph/traversal.js.map

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package/lib/dist/index.d.ts

@@ -7,7 +7,7 @@
 import { Node, Edge, FileRecord, ExtractionResult, Subgraph, TraversalOptions, SearchOptions, SearchResult, Context, GraphStats, TaskInput, TaskContext, BuildContextOptions, FindRelevantContextOptions } from './types';
 import { IndexProgress, IndexResult, SyncResult } from './extraction';
 import { ResolutionResult } from './resolution';
-import { WatchOptions } from './sync';
+import { WatchOptions, PendingFile } from './sync';
 export * from './types';
 export { getDatabasePath } from './db';
 export { getCodeGraphDir, isInitialized, findNearestCodeGraphRoot, CODEGRAPH_DIR, } from './directory';
@@ -16,7 +16,7 @@ export { detectLanguage, isLanguageSupported, isGrammarLoaded, getSupportedLangu
 export { ResolutionResult } from './resolution';
 export { CodeGraphError, FileError, ParseError, DatabaseError, SearchError, VectorError, ConfigError, Logger, setLogger, getLogger, silentLogger, defaultLogger, } from './errors';
 export { Mutex, FileLock, processInBatches, debounce, throttle, MemoryMonitor } from './utils';
-export { FileWatcher, WatchOptions } from './sync';
+export { FileWatcher, WatchOptions, PendingFile } from './sync';
 export { MCPServer } from './mcp';
 /**
  * Options for initializing a new CodeGraph project
@@ -143,6 +143,25 @@ export declare class CodeGraph {
      * Check if the file watcher is active.
      */
     isWatching(): boolean;
+    /**
+     * Files seen by the file watcher since the last successful sync —
+     * the per-file "stale" signal MCP tools attach to responses so an agent
+     * can fall back to {@link Read} for just the affected file without
+     * waiting for a debounced sync to complete (issue #403).
+     *
+     * Returns an empty list when the watcher isn't active, or no events have
+     * arrived. Each entry includes `firstSeenMs` and `lastSeenMs` (wall-clock
+     * `Date.now()` values) so callers can render "edited Nms ago", plus an
+     * `indexing` flag indicating whether the in-flight sync (if any) will
+     * absorb that file.
+     */
+    getPendingFiles(): PendingFile[];
+    /**
+     * Resolves once the file watcher has finished its initial chokidar scan.
+     * Useful for tests that need a deterministic boundary before asserting on
+     * `getPendingFiles()`. Resolves immediately when no watcher is active.
+     */
+    waitUntilWatcherReady(timeoutMs?: number): Promise<void>;
     /**
      * Get files that have changed since last index
      */

package/lib/dist/index.d.ts.map

@@ -1 +1 @@
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package/lib/dist/index.js

@@ -262,6 +262,16 @@ class CodeGraph {
             }
             try {
                 const result = await this.orchestrator.indexAll(options.onProgress, options.signal, options.verbose);
+                // Re-detect frameworks now that the index is populated. The resolver
+                // is constructed with createResolver() before any files exist, so
+                // framework resolvers whose detect() consults the indexed file list
+                // (e.g. UIKit/SwiftUI scanning for imports, swift-objc-bridge looking
+                // for both Swift and ObjC files) all return false on that initial pass
+                // and silently drop themselves. Re-initializing here gives them a
+                // chance to see the actual project before resolution runs.
+                if (result.success && result.filesIndexed > 0) {
+                    this.resolver.initialize();
+                }
                 // Resolve references to create call/import/extends edges
                 if (result.success && result.filesIndexed > 0) {
                     // Get count without loading all refs into memory
@@ -279,6 +289,11 @@ class CodeGraph {
                         });
                     });
                 }
+                // Refresh planner stats + checkpoint the WAL after bulk writes.
+                // Cheap and non-blocking; never load-bearing for correctness.
+                if (result.success && result.filesIndexed > 0) {
+                    this.db.runMaintenance();
+                }
                 return result;
             }
             finally {
@@ -357,6 +372,10 @@ class CodeGraph {
                         });
                     }
                 }
+                // Refresh planner stats + checkpoint the WAL after bulk writes.
+                if (result.filesAdded > 0 || result.filesModified > 0 || result.filesRemoved > 0) {
+                    this.db.runMaintenance();
+                }
                 return result;
             }
             finally {
@@ -407,6 +426,29 @@ class CodeGraph {
     isWatching() {
         return this.watcher?.isActive() ?? false;
     }
+    /**
+     * Files seen by the file watcher since the last successful sync —
+     * the per-file "stale" signal MCP tools attach to responses so an agent
+     * can fall back to {@link Read} for just the affected file without
+     * waiting for a debounced sync to complete (issue #403).
+     *
+     * Returns an empty list when the watcher isn't active, or no events have
+     * arrived. Each entry includes `firstSeenMs` and `lastSeenMs` (wall-clock
+     * `Date.now()` values) so callers can render "edited Nms ago", plus an
+     * `indexing` flag indicating whether the in-flight sync (if any) will
+     * absorb that file.
+     */
+    getPendingFiles() {
+        return this.watcher?.getPendingFiles() ?? [];
+    }
+    /**
+     * Resolves once the file watcher has finished its initial chokidar scan.
+     * Useful for tests that need a deterministic boundary before asserting on
+     * `getPendingFiles()`. Resolves immediately when no watcher is active.
+     */
+    waitUntilWatcherReady(timeoutMs) {
+        return this.watcher ? this.watcher.waitUntilReady(timeoutMs) : Promise.resolve();
+    }
     /**
      * Get files that have changed since last index
      */

package/lib/dist/index.js.map

@@ -1 +1 @@
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package/lib/dist/installer/instructions-template.d.ts

@@ -18,11 +18,11 @@ export declare const CODEGRAPH_SECTION_END = "<!-- CODEGRAPH_END -->";
  * instructions file. Includes the start/end markers so the section
  * can be detected and replaced on re-install.
  */
-export declare const INSTRUCTIONS_TEMPLATE = "<!-- CODEGRAPH_START -->\n## CodeGraph\n\nThis project has a CodeGraph MCP server (`codegraph_*` tools) configured. CodeGraph is a tree-sitter-parsed knowledge graph of every symbol, edge, and file. Reads are sub-millisecond and return structural information grep cannot.\n\n### When to prefer codegraph over native search\n\nUse codegraph for **structural** questions \u2014 what calls what, what would break, where is X defined, what is X's signature. Use native grep/read only for **literal text** queries (string contents, comments, log messages) or after you already have a specific file open.\n\n| Question | Tool |\n|---|---|\n| \"Where is X defined?\" / \"Find symbol named X\" | `codegraph_search` |\n| \"What calls function Y?\" | `codegraph_callers` |\n| \"What does Y call?\" | `codegraph_callees` |\n| \"What would break if I changed Z?\" | `codegraph_impact` |\n| \"Show me Y's signature / source / docstring\" | `codegraph_node` |\n| \"Give me focused context for a task/area\" | `codegraph_context` |\n| \"See several related symbols' source at once\" | `codegraph_explore` |\n| \"What files exist under path/\" | `codegraph_files` |\n| \"Is the index healthy?\" | `codegraph_status` |\n\n### Rules of thumb\n\n- **Answer directly \u2014 don't delegate exploration.** For \"how does X work\" / architecture / trace questions, answer with 2-3 codegraph calls: `codegraph_context` first, then ONE `codegraph_explore` for the source of the symbols it surfaces. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent \u2014 or running a grep + read loop \u2014 repeats work codegraph already did and costs more for the same answer.\n- **Trust codegraph results.** They come from a full AST parse. Do NOT re-verify them with grep \u2014 that's slower, less accurate, and wastes context.\n- **Don't grep first** when looking up a symbol by name. `codegraph_search` is faster and returns kind + location + signature in one call.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one call.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns several symbols' source grouped in a single capped call, while each separate node/Read call re-reads the whole context and costs far more.\n- **Index lag**: the file watcher debounces ~500ms behind writes; don't re-query immediately after editing a file in the same turn.\n\n### If `.codegraph/` doesn't exist\n\nThe MCP server returns \"not initialized.\" Ask the user: *\"I notice this project doesn't have CodeGraph initialized. Want me to run `codegraph init -i` to build the index?\"*\n<!-- CODEGRAPH_END -->";
+export declare const INSTRUCTIONS_TEMPLATE = "<!-- CODEGRAPH_START -->\n## CodeGraph\n\nThis project has a CodeGraph MCP server (`codegraph_*` tools) configured. CodeGraph is a tree-sitter-parsed knowledge graph of every symbol, edge, and file. Reads are sub-millisecond and return structural information grep cannot.\n\n### When to prefer codegraph over native search\n\nUse codegraph for **structural** questions \u2014 what calls what, what would break, where is X defined, what is X's signature. Use native grep/read only for **literal text** queries (string contents, comments, log messages) or after you already have a specific file open.\n\n| Question | Tool |\n|---|---|\n| \"Where is X defined?\" / \"Find symbol named X\" | `codegraph_search` |\n| \"What calls function Y?\" | `codegraph_callers` |\n| \"What does Y call?\" | `codegraph_callees` |\n| \"How does X reach/become Y? / trace the flow from X to Y\" | `codegraph_trace` (one call = the whole path, incl. callback/React/JSX dynamic hops) |\n| \"What would break if I changed Z?\" | `codegraph_impact` |\n| \"Show me Y's signature / source / docstring\" | `codegraph_node` |\n| \"Give me focused context for a task/area\" | `codegraph_context` |\n| \"See several related symbols' source at once\" | `codegraph_explore` |\n| \"What files exist under path/\" | `codegraph_files` |\n| \"Is the index healthy?\" | `codegraph_status` |\n\n### Rules of thumb\n\n- **Answer directly \u2014 don't delegate exploration.** For \"how does X work\" / architecture questions, answer with 2-3 codegraph calls: `codegraph_context` first, then ONE `codegraph_explore` for the source of the symbols it surfaces. For a specific **flow** (\"how does X reach Y\") start with `codegraph_trace` from\u2192to \u2014 one call returns the whole path with dynamic hops bridged \u2014 then ONE `codegraph_explore` for the bodies; don't rebuild the path with `codegraph_search` + `codegraph_callers`. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent \u2014 or running a grep + read loop \u2014 repeats work codegraph already did and costs more for the same answer.\n- **Trust codegraph results.** They come from a full AST parse. Do NOT re-verify them with grep \u2014 that's slower, less accurate, and wastes context.\n- **Don't grep first** when looking up a symbol by name. `codegraph_search` is faster and returns kind + location + signature in one call.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one call.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns several symbols' source grouped in a single capped call, while each separate node/Read call re-reads the whole context and costs far more.\n- **Index lag \u2014 check the staleness banner, don't guess a wait.** When a codegraph response starts with \"\u26A0\uFE0F Some files referenced below were edited since the last index sync\u2026\", the listed files are pending re-index \u2014 Read those specific files for accurate content. Files NOT in that banner are fresh and codegraph is authoritative for them. `codegraph_status` also lists pending files under \"Pending sync\".\n\n### If `.codegraph/` doesn't exist\n\nThe MCP server returns \"not initialized.\" Ask the user: *\"I notice this project doesn't have CodeGraph initialized. Want me to run `codegraph init -i` to build the index?\"*\n<!-- CODEGRAPH_END -->";
 /**
  * Backwards-compat alias. Existing downstream code may import
  * `CLAUDE_MD_TEMPLATE` from this module via the re-export shim in
  * `claude-md-template.ts`.
  */
-export declare const CLAUDE_MD_TEMPLATE = "<!-- CODEGRAPH_START -->\n## CodeGraph\n\nThis project has a CodeGraph MCP server (`codegraph_*` tools) configured. CodeGraph is a tree-sitter-parsed knowledge graph of every symbol, edge, and file. Reads are sub-millisecond and return structural information grep cannot.\n\n### When to prefer codegraph over native search\n\nUse codegraph for **structural** questions \u2014 what calls what, what would break, where is X defined, what is X's signature. Use native grep/read only for **literal text** queries (string contents, comments, log messages) or after you already have a specific file open.\n\n| Question | Tool |\n|---|---|\n| \"Where is X defined?\" / \"Find symbol named X\" | `codegraph_search` |\n| \"What calls function Y?\" | `codegraph_callers` |\n| \"What does Y call?\" | `codegraph_callees` |\n| \"What would break if I changed Z?\" | `codegraph_impact` |\n| \"Show me Y's signature / source / docstring\" | `codegraph_node` |\n| \"Give me focused context for a task/area\" | `codegraph_context` |\n| \"See several related symbols' source at once\" | `codegraph_explore` |\n| \"What files exist under path/\" | `codegraph_files` |\n| \"Is the index healthy?\" | `codegraph_status` |\n\n### Rules of thumb\n\n- **Answer directly \u2014 don't delegate exploration.** For \"how does X work\" / architecture / trace questions, answer with 2-3 codegraph calls: `codegraph_context` first, then ONE `codegraph_explore` for the source of the symbols it surfaces. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent \u2014 or running a grep + read loop \u2014 repeats work codegraph already did and costs more for the same answer.\n- **Trust codegraph results.** They come from a full AST parse. Do NOT re-verify them with grep \u2014 that's slower, less accurate, and wastes context.\n- **Don't grep first** when looking up a symbol by name. `codegraph_search` is faster and returns kind + location + signature in one call.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one call.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns several symbols' source grouped in a single capped call, while each separate node/Read call re-reads the whole context and costs far more.\n- **Index lag**: the file watcher debounces ~500ms behind writes; don't re-query immediately after editing a file in the same turn.\n\n### If `.codegraph/` doesn't exist\n\nThe MCP server returns \"not initialized.\" Ask the user: *\"I notice this project doesn't have CodeGraph initialized. Want me to run `codegraph init -i` to build the index?\"*\n<!-- CODEGRAPH_END -->";
+export declare const CLAUDE_MD_TEMPLATE = "<!-- CODEGRAPH_START -->\n## CodeGraph\n\nThis project has a CodeGraph MCP server (`codegraph_*` tools) configured. CodeGraph is a tree-sitter-parsed knowledge graph of every symbol, edge, and file. Reads are sub-millisecond and return structural information grep cannot.\n\n### When to prefer codegraph over native search\n\nUse codegraph for **structural** questions \u2014 what calls what, what would break, where is X defined, what is X's signature. Use native grep/read only for **literal text** queries (string contents, comments, log messages) or after you already have a specific file open.\n\n| Question | Tool |\n|---|---|\n| \"Where is X defined?\" / \"Find symbol named X\" | `codegraph_search` |\n| \"What calls function Y?\" | `codegraph_callers` |\n| \"What does Y call?\" | `codegraph_callees` |\n| \"How does X reach/become Y? / trace the flow from X to Y\" | `codegraph_trace` (one call = the whole path, incl. callback/React/JSX dynamic hops) |\n| \"What would break if I changed Z?\" | `codegraph_impact` |\n| \"Show me Y's signature / source / docstring\" | `codegraph_node` |\n| \"Give me focused context for a task/area\" | `codegraph_context` |\n| \"See several related symbols' source at once\" | `codegraph_explore` |\n| \"What files exist under path/\" | `codegraph_files` |\n| \"Is the index healthy?\" | `codegraph_status` |\n\n### Rules of thumb\n\n- **Answer directly \u2014 don't delegate exploration.** For \"how does X work\" / architecture questions, answer with 2-3 codegraph calls: `codegraph_context` first, then ONE `codegraph_explore` for the source of the symbols it surfaces. For a specific **flow** (\"how does X reach Y\") start with `codegraph_trace` from\u2192to \u2014 one call returns the whole path with dynamic hops bridged \u2014 then ONE `codegraph_explore` for the bodies; don't rebuild the path with `codegraph_search` + `codegraph_callers`. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent \u2014 or running a grep + read loop \u2014 repeats work codegraph already did and costs more for the same answer.\n- **Trust codegraph results.** They come from a full AST parse. Do NOT re-verify them with grep \u2014 that's slower, less accurate, and wastes context.\n- **Don't grep first** when looking up a symbol by name. `codegraph_search` is faster and returns kind + location + signature in one call.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one call.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns several symbols' source grouped in a single capped call, while each separate node/Read call re-reads the whole context and costs far more.\n- **Index lag \u2014 check the staleness banner, don't guess a wait.** When a codegraph response starts with \"\u26A0\uFE0F Some files referenced below were edited since the last index sync\u2026\", the listed files are pending re-index \u2014 Read those specific files for accurate content. Files NOT in that banner are fresh and codegraph is authoritative for them. `codegraph_status` also lists pending files under \"Pending sync\".\n\n### If `.codegraph/` doesn't exist\n\nThe MCP server returns \"not initialized.\" Ask the user: *\"I notice this project doesn't have CodeGraph initialized. Want me to run `codegraph init -i` to build the index?\"*\n<!-- CODEGRAPH_END -->";
 //# sourceMappingURL=instructions-template.d.ts.map

package/lib/dist/installer/instructions-template.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"instructions-template.d.ts","sourceRoot":"","sources":["../../src/installer/instructions-template.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,4DAA4D;AAC5D,eAAO,MAAM,uBAAuB,6BAA6B,CAAC;AAClE,eAAO,MAAM,qBAAqB,2BAA2B,CAAC;AAE9D;;;;GAIG;AACH,eAAO,MAAM,qBAAqB,y2GAkCT,CAAC;AAE1B;;;;GAIG;AACH,eAAO,MAAM,kBAAkB,y2GAAwB,CAAC"}

package/lib/dist/installer/instructions-template.js

@@ -35,6 +35,7 @@ Use codegraph for **structural** questions — what calls what, what would break
 | "Where is X defined?" / "Find symbol named X" | \`codegraph_search\` |
 | "What calls function Y?" | \`codegraph_callers\` |
 | "What does Y call?" | \`codegraph_callees\` |
+| "How does X reach/become Y? / trace the flow from X to Y" | \`codegraph_trace\` (one call = the whole path, incl. callback/React/JSX dynamic hops) |
 | "What would break if I changed Z?" | \`codegraph_impact\` |
 | "Show me Y's signature / source / docstring" | \`codegraph_node\` |
 | "Give me focused context for a task/area" | \`codegraph_context\` |
@@ -44,12 +45,12 @@ Use codegraph for **structural** questions — what calls what, what would break
 
 ### Rules of thumb
 
-- **Answer directly — don't delegate exploration.** For "how does X work" / architecture / trace questions, answer with 2-3 codegraph calls: \`codegraph_context\` first, then ONE \`codegraph_explore\` for the source of the symbols it surfaces. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent — or running a grep + read loop — repeats work codegraph already did and costs more for the same answer.
+- **Answer directly — don't delegate exploration.** For "how does X work" / architecture questions, answer with 2-3 codegraph calls: \`codegraph_context\` first, then ONE \`codegraph_explore\` for the source of the symbols it surfaces. For a specific **flow** ("how does X reach Y") start with \`codegraph_trace\` from→to — one call returns the whole path with dynamic hops bridged — then ONE \`codegraph_explore\` for the bodies; don't rebuild the path with \`codegraph_search\` + \`codegraph_callers\`. Codegraph IS the pre-built index, so spawning a separate file-reading sub-task/agent — or running a grep + read loop — repeats work codegraph already did and costs more for the same answer.
 - **Trust codegraph results.** They come from a full AST parse. Do NOT re-verify them with grep — that's slower, less accurate, and wastes context.
 - **Don't grep first** when looking up a symbol by name. \`codegraph_search\` is faster and returns kind + location + signature in one call.
 - **Don't chain \`codegraph_search\` + \`codegraph_node\`** when you just want context — \`codegraph_context\` is one call.
 - **Don't loop \`codegraph_node\` over many symbols** — one \`codegraph_explore\` call returns several symbols' source grouped in a single capped call, while each separate node/Read call re-reads the whole context and costs far more.
-- **Index lag**: the file watcher debounces ~500ms behind writes; don't re-query immediately after editing a file in the same turn.
+- **Index lag — check the staleness banner, don't guess a wait.** When a codegraph response starts with "⚠️ Some files referenced below were edited since the last index sync…", the listed files are pending re-index — Read those specific files for accurate content. Files NOT in that banner are fresh and codegraph is authoritative for them. \`codegraph_status\` also lists pending files under "Pending sync".
 
 ### If \`.codegraph/\` doesn't exist
 

package/lib/dist/installer/instructions-template.js.map

@@ -1 +1 @@
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