@colbymchenry/codegraph-darwin-x64 0.9.5 → 0.9.7

package/lib/dist/mcp/tools.js

@@ -48,7 +48,9 @@ const worktree_1 = require("../sync/worktree");
 const crypto_1 = require("crypto");
 const fs_1 = require("fs");
 const utils_1 = require("../utils");
+const generated_detection_1 = require("../extraction/generated-detection");
 const os_1 = require("os");
+const pathModule = __importStar(require("path"));
 const path_1 = require("path");
 /** Maximum output length to prevent context bloat (characters) */
 const MAX_OUTPUT_LENGTH = 15000;
@@ -105,18 +107,40 @@ function getExploreBudget(fileCount) {
     return 5;
 }
 function getExploreOutputBudget(fileCount) {
+    if (fileCount < 150) {
+        return {
+            // ITER3: revert iter2's aggressive body shrink (forced Read fallback —
+            // the per-file 2.5K cap pushed the agent to Read instead of node).
+            // Back to the iter1 shape (13K/4/3.8K) but keep the test-file
+            // hard-exclude. The cost lever for this tier lives in handleContext
+            // (steering the agent to stop after 1-2 calls), not in this budget.
+            maxOutputChars: 13000,
+            defaultMaxFiles: 4,
+            maxCharsPerFile: 3800,
+            gapThreshold: 7,
+            maxSymbolsInFileHeader: 5,
+            maxEdgesPerRelationshipKind: 4,
+            includeRelationships: false,
+            includeAdditionalFiles: false,
+            includeCompletenessSignal: false,
+            includeBudgetNote: false,
+            excludeLowValueFiles: true,
+        };
+    }
     if (fileCount < 500) {
         return {
+            // ITER3: same revert/keep-filter pattern as <150.
             maxOutputChars: 18000,
             defaultMaxFiles: 5,
             maxCharsPerFile: 3800,
             gapThreshold: 8,
             maxSymbolsInFileHeader: 6,
             maxEdgesPerRelationshipKind: 6,
-            includeRelationships: true,
+            includeRelationships: false,
             includeAdditionalFiles: false,
             includeCompletenessSignal: false,
             includeBudgetNote: false,
+            excludeLowValueFiles: true,
         };
     }
     if (fileCount < 5000) {
@@ -136,6 +160,7 @@ function getExploreOutputBudget(fileCount) {
             includeAdditionalFiles: true,
             includeCompletenessSignal: true,
             includeBudgetNote: true,
+            excludeLowValueFiles: false,
         };
     }
     if (fileCount < 15000) {
@@ -150,6 +175,7 @@ function getExploreOutputBudget(fileCount) {
             includeAdditionalFiles: true,
             includeCompletenessSignal: true,
             includeBudgetNote: true,
+            excludeLowValueFiles: false,
         };
     }
     return {
@@ -163,6 +189,7 @@ function getExploreOutputBudget(fileCount) {
         includeAdditionalFiles: true,
         includeCompletenessSignal: true,
         includeBudgetNote: true,
+        excludeLowValueFiles: false,
     };
 }
 /**
@@ -323,7 +350,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_context',
-        description: 'PRIMARY TOOL — call this FIRST for any "how does X work", architecture, feature, or bug-context question. Composes search + node + callers + callees and returns entry points, related symbols, and key code in ONE call — usually enough to answer with no further search/Read/Grep. Prefer this over chaining codegraph_search + codegraph_node, and over codegraph_explore. NOTE: provides CODE context, not product requirements; for new features still clarify UX/edge cases with the user.',
+        description: 'PRIMARY TOOL — call FIRST for any "how does X work"/architecture/bug question. Returns entry points + related symbols + key code in one call; usually answers without further search/Read/Grep. Provides CODE context, not product requirements.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -348,7 +375,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_callers',
-        description: 'Find all functions/methods that call a specific symbol. Useful for understanding usage patterns and impact of changes.',
+        description: 'List functions that call <symbol>. For deep flow use codegraph_trace.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -368,7 +395,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_callees',
-        description: 'Find all functions/methods that a specific symbol calls. Useful for understanding dependencies and code flow.',
+        description: 'List functions that <symbol> calls. For deep flow use codegraph_trace.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -388,7 +415,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_impact',
-        description: 'Analyze the impact radius of changing a symbol. Shows what code could be affected by modifications.',
+        description: 'List symbols affected by changing <symbol>. Use before a refactor.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -408,7 +435,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_node',
-        description: 'Get ONE symbol\'s details (location, signature, docstring) PLUS its TRAIL — what it calls and what calls it, each with file:line. Pass includeCode=true for source (functions return their body; containers return a member outline). Use this to WALK the call graph hop-by-hop — node a symbol, then node one of its trail entries — the structural, no-Read way to follow "what calls/triggers/handles X" across files. For a broad first overview of many symbols at once use codegraph_explore; use node to drill along a specific path from there. (If a trail is empty on a non-leaf, that hop is likely dynamic dispatch — read just that line.) Source returned with includeCode is the verbatim live file content — identical to Read.',
+        description: 'One symbol\'s location, signature, callers/callees trail. includeCode=true returns the verbatim body. Use codegraph_trace for full paths instead of chaining nodes.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -428,7 +455,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_explore',
-        description: 'Returns source for SEVERAL related symbols grouped by file, plus a relationship map, in ONE capped call. This is the efficient way to inspect many related symbols at once — strongly prefer it over a series of codegraph_node or Read calls (each separate call re-reads the whole context, so 8 node calls cost far more than 1 explore). Use it after codegraph_context when you need to see the actual source of several symbols. Query with specific symbol/file/code terms, NOT natural-language sentences — run codegraph_search first to find names. Bad: "how are agent prompts loaded and passed to the CLI". Good: "renderStaticScene drawElementOnCanvas ShapeCache renderElement.ts". The code it returns is the VERBATIM live file source (byte-for-byte identical to Read), line-numbered — not a summary; treat files it shows as already Read, no need to re-open them.',
+        description: 'Source of SEVERAL related symbols grouped by file, in one capped call. Query is a bag of symbol/file names (not a question). Returned source is verbatim Read-equivalent — do not re-open shown files. Prefer over chained codegraph_node.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -448,7 +475,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_status',
-        description: 'Get the status of the CodeGraph index, including statistics about indexed files, nodes, and edges.',
+        description: 'Index health check (files / nodes / edges). Skip unless debugging.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -458,7 +485,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_files',
-        description: 'REQUIRED for file/folder exploration. Get the project file structure from the CodeGraph index. Returns a tree view of all indexed files with metadata (language, symbol count). Much faster than Glob/filesystem scanning. Use this FIRST when exploring project structure, finding files, or understanding codebase organization.',
+        description: 'Indexed file tree with language + symbol counts. Faster than Glob for project layout.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -491,7 +518,7 @@ exports.tools = [
     },
     {
         name: 'codegraph_trace',
-        description: 'Trace the CALL PATH between two symbols — "how does <from> reach/become <to>?" Returns the chain of functions from one to the other (each hop with file:line and its body inlined, plus the outgoing calls of the destination itself) in ONE call. This is something grep/Read structurally cannot do: there is no text pattern for "the path from A to B". Ideal for flow questions — how an update triggers a render, how a request reaches a handler, how a QuerySet becomes SQL. If no static path exists the chain likely breaks at dynamic dispatch (callbacks/descriptors/metaclasses); the tool says where and points you to codegraph_node to bridge it.',
+        description: 'Call path between two symbols — "how does <from> reach <to>?" Returns the chain with each hop\'s body inlined plus the destination\'s callees, in ONE call. Ideal for flow questions (update→render, request→handler, QuerySet→SQL). If no static path exists the chain broke at dynamic dispatch — the failure response inlines both endpoints + their TO-file siblings.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -528,6 +555,14 @@ class ToolHandler {
     // once and every later tool call reuses the result — never shelling out to
     // git on the hot path. `undefined` = not computed yet; `null` = no mismatch.
     worktreeMismatchCache = new Map();
+    // Gate that the MCP engine pokes after `cg.open()` so the first tool call
+    // blocks on the post-open filesystem reconcile (catch-up sync). Without
+    // this, a tool call that races past `catchUpSync()` serves rows for files
+    // that were deleted (or edited) while no MCP server was running — and the
+    // per-file staleness banner can't help, because `getPendingFiles()` is
+    // populated by the watcher, not by catch-up. Cleared on first await so
+    // subsequent calls don't pay any cost.
+    catchUpGate = null;
     constructor(cg) {
         this.cg = cg;
     }
@@ -537,6 +572,16 @@ class ToolHandler {
     setDefaultCodeGraph(cg) {
         this.cg = cg;
     }
+    /**
+     * Engine-only: register the catch-up sync promise so the next `execute()`
+     * call awaits it before serving. The handler swallows rejections (the
+     * engine logs them) so a sync failure never propagates as a tool error;
+     * we still want to serve a best-effort result over the same potentially-
+     * stale data, which is what would have happened without the gate.
+     */
+    setCatchUpGate(p) {
+        this.catchUpGate = p;
+    }
     /**
      * Record the directory the server tried to resolve the default project from.
      * Used only to make the "no default project" error actionable.
@@ -579,7 +624,7 @@ class ToolHandler {
      */
     getTools() {
         const allow = this.toolAllowlist();
-        const visible = allow
+        let visible = allow
             ? exports.tools.filter(t => allow.has(t.name.replace(/^codegraph_/, '')))
             : exports.tools;
         if (!this.cg)
@@ -587,6 +632,39 @@ class ToolHandler {
         try {
             const stats = this.cg.getStats();
             const budget = getExploreBudget(stats.fileCount);
+            // Tiny-repo tool gating: on projects under TINY_REPO_FILE_THRESHOLD
+            // files, only expose the 5 core tools (search, context, node,
+            // explore, trace). The 5 omitted tools (callers, callees, impact,
+            // status, files) reduce to one grep at this scale.
+            //
+            // n=2 audits ruled out cutting below 5 tools:
+            // - 3-tool gate (search + context + trace): cost regressed on
+            //   cobra/ky/sinatra. The agent fell back to raw Reads to cover
+            //   what codegraph_node + codegraph_explore would have answered.
+            // - 1-tool gate (search only): catastrophic regression — express
+            //   went from -43% WIN to +107% LOSS. With only search, the agent
+            //   can't navigate the call graph structurally and reads everything.
+            //
+            // 5 is the empirical lower bound. Tools beyond search/context/
+            // node/explore/trace pay overhead that the agent doesn't recoup
+            // on tiny-repo flow questions.
+            // ITER4: raise threshold 150 → 500 so single-file frameworks
+            // (sinatra at 159, slim_framework around 200) also get the
+            // 5-tool surface. The empirical 5-tool floor was set on <150
+            // probes; iter3 measurement showed sinatra is structurally the
+            // SAME problem as cobra (single-file WITHOUT-arm Read wins),
+            // so it deserves the same gating.
+            const TINY_REPO_FILE_THRESHOLD = 500;
+            const TINY_REPO_CORE_TOOLS = new Set([
+                'codegraph_search',
+                'codegraph_context',
+                'codegraph_node',
+                'codegraph_explore',
+                'codegraph_trace',
+            ]);
+            if (stats.fileCount < TINY_REPO_FILE_THRESHOLD) {
+                visible = visible.filter(t => TINY_REPO_CORE_TOOLS.has(t.name));
+            }
             return visible.map(tool => {
                 if (tool.name === 'codegraph_explore') {
                     return {
@@ -842,6 +920,19 @@ class ToolHandler {
      */
     async execute(toolName, args) {
         try {
+            // Block the first tool call on the engine's post-open reconcile so we
+            // never serve rows for files deleted/edited while no MCP server was
+            // running. The gate is cleared after first await — subsequent calls
+            // pay nothing. Catch-up failures are logged by the engine; we
+            // proceed regardless so a transient sync error never breaks tools.
+            if (this.catchUpGate) {
+                const gate = this.catchUpGate;
+                this.catchUpGate = null;
+                try {
+                    await gate;
+                }
+                catch { /* engine already logged */ }
+            }
             // Honor the optional tool allowlist (CODEGRAPH_MCP_TOOLS): a trimmed
             // surface rejects ablated tools defensively even if a client cached them.
             if (!this.isToolAllowed(toolName)) {
@@ -935,7 +1026,15 @@ class ToolHandler {
         if (results.length === 0) {
             return this.textResult(`No results found for "${query}"`);
         }
-        const formatted = this.formatSearchResults(results);
+        // Down-rank generated files within the FTS-returned set so a search
+        // for "Send" surfaces the hand-written keeper before .pb.go stubs
+        // that share the name. Stable: only reorders generated vs. not.
+        const ranked = [...results].sort((a, b) => {
+            const aGen = (0, generated_detection_1.isGeneratedFile)(a.node.filePath) ? 1 : 0;
+            const bGen = (0, generated_detection_1.isGeneratedFile)(b.node.filePath) ? 1 : 0;
+            return aGen - bGen;
+        });
+        const formatted = this.formatSearchResults(ranked);
         return this.textResult(this.truncateOutput(formatted));
     }
     /**
@@ -951,7 +1050,27 @@ class ToolHandler {
             markSessionConsulted(sessionId);
         }
         const cg = this.getCodeGraph(args.projectPath);
-        const maxNodes = args.maxNodes || 20;
+        // On tiny repos (<150 files), trim maxNodes hard — the entire repo
+        // is grep-able in a turn so a 20-node context is wasted budget.
+        // 8 covers the typical 1-3 entry-point + their immediate neighbors
+        // without dragging in the rest of the small codebase.
+        let defaultMaxNodes = 20;
+        let isTinyRepo = false;
+        let isSmallRepo = false;
+        try {
+            const stats = cg.getStats();
+            if (stats.fileCount < 150) {
+                defaultMaxNodes = 8;
+                isTinyRepo = true;
+            }
+            else if (stats.fileCount < 500) {
+                isSmallRepo = true;
+            }
+        }
+        catch {
+            // stats failure — fall back to the standard default
+        }
+        const maxNodes = args.maxNodes || defaultMaxNodes;
         const includeCode = args.includeCode !== false;
         const context = await cg.buildContext(task, {
             maxNodes,
@@ -963,12 +1082,189 @@ class ToolHandler {
         const reminder = isFeatureQuery
             ? '\n\n⚠️ **Ask user:** UX preferences, edge cases, acceptance criteria'
             : '';
+        // Auto-trace for flow queries: when the task is asking "how does X
+        // reach/flow/propagate from A to B", run the trace internally and
+        // append its body to the context response. Saves the agent the
+        // follow-up codegraph_trace call that was the #2 cost driver on
+        // multi-module flow questions (Q3 / etcd Q2 in the audit).
+        const flowTrace = await this.maybeInlineFlowTrace(task, cg);
+        // Iter3 — sufficiency steering on small repos.
+        //
+        // Measured economics on tiny (<150) and small (<500) projects: every
+        // additional MCP tool call costs ~$0.02-0.05 in cache-write tokens
+        // (5K-15K per response at $3.75/1M). The agent reflexively follows
+        // codegraph_context with explore/node even when the context response
+        // is already sufficient — that pattern drove the cost gap that
+        // smaller bodies (iter2) failed to close (smaller bodies just shifted
+        // the agent to Read instead). Direct directive on small-repo
+        // responses: tell the agent the context call IS the comprehensive
+        // pass for a project of this size and that follow-ups should be
+        // narrow (trace from→to, node single-symbol) — not another broad
+        // explore that re-bundles the same content.
+        // ITER4: unified strong directive for both tiny (<150) and small
+        // (<500) tiers — measured iter3 result was that the soft <500
+        // wording was IGNORED on sinatra (5 tool calls, +92% loss) while
+        // the strong <150 wording was followed on cobra/slim (3 calls,
+        // -21%/-22% wins). The single-file-framework problem (sinatra)
+        // is structurally the same as cobra's; both deserve the same
+        // sufficiency steering.
+        let smallRepoTail = '';
+        let smallRepoRouteInline = '';
+        if (isTinyRepo || isSmallRepo) {
+            // Iter12: backend-computed routing manifest for routing queries.
+            // Builds a URL → handler map directly from the graph (each route
+            // node has a `references` edge to its handler), then inlines the
+            // top handler file's source. The agent gets the canonical
+            // routing answer in one MCP call — no need to parse framework
+            // DSL or grep for handlers.
+            //
+            // Replaces iter10's raw route-file inline. The manifest is more
+            // information-dense (parsed URL→handler map vs raw config DSL)
+            // and we still inline the top handler file's source so the agent
+            // has the implementation bodies inline too.
+            const isRouteQuery = /\b(route|routes|routing|request|handler|endpoint|api|controller|middleware|dispatch|invok)/i.test(task);
+            if (isRouteQuery) {
+                try {
+                    const manifest = cg.getRoutingManifest(40);
+                    if (manifest) {
+                        // 1) Compact URL→handler list (~30-60 lines, ~1-2KB).
+                        const lines = [
+                            `\n\n## Routing manifest (${manifest.totalRoutes} routes, top handler file holds ${manifest.topHandlerFileCount})`,
+                            '',
+                            '| URL | Handler | Location |',
+                            '|---|---|---|',
+                        ];
+                        for (const e of manifest.entries) {
+                            lines.push(`| \`${e.url}\` | \`${e.handler}\` | ${e.handlerFile}:${e.handlerLine} |`);
+                        }
+                        // 2) Inline the top handler file's source.
+                        if (manifest.topHandlerFile && manifest.topHandlerFileCount >= 2) {
+                            try {
+                                const fullPath = pathModule.join(cg.getProjectRoot(), manifest.topHandlerFile);
+                                const stat = (0, fs_1.statSync)(fullPath);
+                                if (stat.size > 0 && stat.size <= 16000) {
+                                    const source = (0, fs_1.readFileSync)(fullPath, 'utf-8');
+                                    const capped = source.length > 7000 ? source.slice(0, 7000) + '\n... (truncated)' : source;
+                                    const ext = (manifest.topHandlerFile.match(/\.([a-z]+)$/i)?.[1] || '').toLowerCase();
+                                    const lang = ext === 'rb' ? 'ruby' : ext === 'py' ? 'python' :
+                                        ext === 'go' ? 'go' : ext === 'rs' ? 'rust' :
+                                            ext === 'js' || ext === 'jsx' ? 'javascript' :
+                                                ext === 'ts' || ext === 'tsx' ? 'typescript' :
+                                                    ext === 'java' ? 'java' : ext === 'kt' ? 'kotlin' :
+                                                        ext === 'cs' ? 'csharp' : ext === 'php' ? 'php' :
+                                                            ext === 'swift' ? 'swift' : ext === 'yml' || ext === 'yaml' ? 'yaml' : '';
+                                    lines.push('');
+                                    lines.push(`### Top handler file (\`${manifest.topHandlerFile}\` — ${manifest.topHandlerFileCount}/${manifest.totalRoutes} routes, full source inlined — do NOT Read)`);
+                                    lines.push('');
+                                    lines.push('```' + lang);
+                                    lines.push(capped);
+                                    lines.push('```');
+                                }
+                            }
+                            catch { /* file read failed, skip the source inline */ }
+                        }
+                        smallRepoRouteInline = lines.join('\n');
+                    }
+                }
+                catch {
+                    // Manifest build failed — drop silently
+                }
+            }
+            const sizeQualifier = isTinyRepo ? 'under 150' : 'under 500';
+            const routingClause = smallRepoRouteInline
+                ? ' The URL→handler manifest and top handler file are also inlined above — answer routing questions from them.'
+                : '';
+            smallRepoTail = `\n\n---\n> **This project is small** (${sizeQualifier} indexed files). The entry points and code above cover the relevant surface — **do NOT call codegraph_explore as a follow-up; its content will largely duplicate this response**. If you need a specific flow, call \`codegraph_trace from→to\`. If you need one specific symbol's body, call \`codegraph_node <name>\`.${routingClause} Otherwise, answer from what is above.`;
+        }
         // buildContext returns string when format is 'markdown'
         if (typeof context === 'string') {
-            return this.textResult(this.truncateOutput(context + reminder));
+            return this.textResult(this.truncateOutput(context + flowTrace + reminder + smallRepoRouteInline + smallRepoTail));
         }
         // If it returns TaskContext, format it
-        return this.textResult(this.truncateOutput(this.formatTaskContext(context) + reminder));
+        return this.textResult(this.truncateOutput(this.formatTaskContext(context) + flowTrace + reminder + smallRepoRouteInline + smallRepoTail));
+    }
+    /**
+     * Detect a flow-style task ("how does X reach Y", "trace the path from A to B")
+     * and pre-run trace between the most likely endpoints, returning the trace
+     * body to splice into the context response. Returns '' for non-flow queries
+     * or when no plausible endpoint pair can be extracted.
+     *
+     * Conservative by design: only fires when the task has both a clear flow
+     * keyword AND at least two distinct PascalCase / camelCase identifiers.
+     * False positives waste a graph query; false negatives just fall back to
+     * the agent calling trace itself (existing path-proximity wiring handles
+     * disambiguation either way).
+     */
+    async maybeInlineFlowTrace(task, cg) {
+        const lower = task.toLowerCase();
+        const FLOW_KEYWORDS = [
+            'trace ',
+            'from ',
+            'reach ',
+            'flow ',
+            'propagat',
+            'how does ',
+            'how do ',
+        ];
+        if (!FLOW_KEYWORDS.some((k) => lower.includes(k)))
+            return '';
+        // Extract candidate symbols — PascalCase or camelCase identifiers ≥3 chars.
+        // Filter out common non-symbol words and the flow keywords themselves.
+        const STOP_WORDS = new Set([
+            'how', 'does', 'the', 'and', 'from', 'through', 'reach', 'reaches',
+            'flow', 'path', 'trace', 'cross', 'module', 'modules', 'where',
+            'update', 'updates', 'updated', 'when', 'what', 'this', 'that',
+        ]);
+        const ids = [];
+        const seen = new Set();
+        const re = /\b([A-Z][a-z]+(?:[A-Z][a-z]*)+|[a-z]+[A-Z][a-z]*(?:[A-Z][a-z]*)*)\b/g;
+        let m;
+        while ((m = re.exec(task)) !== null) {
+            const sym = m[1];
+            if (sym.length < 3)
+                continue;
+            const key = sym.toLowerCase();
+            if (STOP_WORDS.has(key) || seen.has(key))
+                continue;
+            seen.add(key);
+            ids.push(sym);
+        }
+        if (ids.length < 2)
+            return '';
+        // The first two distinct symbols, in order of appearance, are the most
+        // likely from/to endpoints — "from X ... through to Y" naturally places
+        // them in that order in the prose. If the trace fails to connect, it
+        // still returns the inlined endpoint bodies (the trace-failure rewrite).
+        const fromSym = ids[0];
+        const toSym = ids[1];
+        let traceResult;
+        try {
+            traceResult = await this.handleTrace({
+                from: fromSym,
+                to: toSym,
+                projectPath: cg.getProjectRoot(),
+            });
+        }
+        catch {
+            return '';
+        }
+        // Extract the textual body. Defensive: handleTrace's contract is the
+        // standard tool-result shape used elsewhere in this file.
+        const body = traceResult.content
+            ?.map((c) => (c.type === 'text' ? c.text : ''))
+            .filter(Boolean)
+            .join('\n')
+            .trim();
+        if (!body)
+            return '';
+        return [
+            '',
+            '## Inline flow trace',
+            '',
+            `Auto-traced \`${fromSym}\` → \`${toSym}\` because the query looks like a flow question. No follow-up codegraph_trace is needed for this pair.`,
+            '',
+            body,
+        ].join('\n');
     }
     /**
      * Heuristic to detect if a query looks like a feature request
@@ -1130,46 +1426,180 @@ class ToolHandler {
         // (which, on real code, means the flow breaks at dynamic dispatch).
         const edgeKinds = ['calls'];
         const MAX_HOPS = 7;
-        const fromTry = fromMatches.nodes.slice(0, 3);
-        const toTry = toMatches.nodes.slice(0, 3);
+        // Path-proximity pairing: in a multi-module repo a symbol name like
+        // `EndBlocker` exists in 20+ modules. FTS picks one almost arbitrarily;
+        // the WRONG pair (e.g. simapp's wrapper EndBlocker paired with gov's Tally)
+        // has no static path, falls through to the dynamic-dispatch failure branch,
+        // and surfaces unrelated bodies — exactly the cosmos-Q3 trace failure mode.
+        // Score every from×to combo by shared file-path prefix length; try the
+        // most-co-located pair first (e.g. `x/gov/abci.go::EndBlocker` ×
+        // `x/gov/keeper/tally.go::Tally` share `x/gov/`).
+        //
+        // Consider the FULL candidate set, not just the FTS top-5: the right
+        // EndBlocker for a gov-module flow may rank 8th in FTS but share the
+        // entire `x/gov/` prefix with the destination. Path-proximity supersedes
+        // FTS for this disambiguation. Findpath trials are still capped by
+        // FINDPATH_PAIR_BUDGET below to bound graph traversal cost.
+        const sharedDirPrefixLen = (a, b) => {
+            const aDir = a.replace(/[^/]+$/, '');
+            const bDir = b.replace(/[^/]+$/, '');
+            let i = 0;
+            while (i < aDir.length && i < bDir.length && aDir[i] === bDir[i])
+                i++;
+            return i;
+        };
+        // Cosmos-Q3 surfaced a second-order failure: `enterprise/group/x/group/`
+        // SHARES MORE of its path with `enterprise/group/x/group/keeper/tally.go`
+        // (24 chars) than `x/gov/abci.go` shares with `x/gov/keeper/tally.go`
+        // (6 chars), so pure shared-prefix prefers the side-experiment module
+        // over the canonical one — even though the user's question is clearly
+        // about the main gov module. Penalize candidates living under prefixes
+        // that conventionally hold extensions / experiments / vendored code, so
+        // the canonical-path pair wins even when its shared prefix is short.
+        const isLessCanonicalPath = (p) => /^(enterprise|contrib|examples?|sample|playground|vendor|third[_-]?party|deprecated|legacy)\//i.test(p);
+        const LESS_CANONICAL_PENALTY = 100; // any canonical candidate beats any less-canonical one
+        const scorePair = (a, b) => sharedDirPrefixLen(a, b)
+            - (isLessCanonicalPath(a) ? LESS_CANONICAL_PENALTY : 0)
+            - (isLessCanonicalPath(b) ? LESS_CANONICAL_PENALTY : 0);
+        const fromCands = fromMatches.nodes;
+        const toCands = toMatches.nodes;
+        const pairs = [];
+        for (const f of fromCands) {
+            for (const t of toCands) {
+                pairs.push({ f, t, score: scorePair(f.filePath, t.filePath) });
+            }
+        }
+        // Sort by shared prefix desc, then by FTS order (already encoded in the
+        // pairs' insertion order — both for f and t). The tiebreaker preserves
+        // findAllSymbols' generated-file-last ranking.
+        pairs.sort((a, b) => b.score - a.score);
+        // Cap how many graph-path probes we attempt so a 50×50 cross-product
+        // doesn't blow up on a god-named symbol like `Get` (well-named flows have
+        // their good pair near the top of the sort anyway).
+        const FINDPATH_PAIR_BUDGET = 20;
+        const fromTry = fromCands;
+        const toTry = toCands;
         let path = null;
         let overCap = null;
-        for (const f of fromTry) {
-            for (const t of toTry) {
-                const p = cg.findPath(f.id, t.id, edgeKinds);
-                if (!p || p.length <= 1)
-                    continue;
+        let bestPair = null;
+        let triedPairs = 0;
+        for (const { f, t } of pairs) {
+            if (path)
+                break;
+            if (triedPairs >= FINDPATH_PAIR_BUDGET)
+                break;
+            triedPairs++;
+            const p = cg.findPath(f.id, t.id, edgeKinds);
+            if (p && p.length > 1) {
                 if (p.length <= MAX_HOPS) {
                     path = p;
+                    bestPair = { f, t };
                     break;
                 }
-                if (!overCap || p.length < overCap.length)
+                if (!overCap || p.length < overCap.length) {
                     overCap = p;
+                    bestPair = { f, t };
+                }
+            }
+            else if (!bestPair) {
+                // No path yet — remember the top-scored pair so the failure branch
+                // surfaces the most-co-located candidates' bodies, not whatever FTS
+                // happened to put first.
+                bestPair = { f, t };
             }
-            if (path)
-                break;
         }
         if (!path) {
-            // No static path — almost always a dynamic-dispatch break. Surface the
-            // start symbol's outgoing calls so the agent can bridge the gap.
-            const start = fromTry[0];
-            const callees = cg.getCallees(start.id).slice(0, 10)
-                .map(c => `${c.node.name} (${c.node.filePath}:${c.node.startLine})`);
+            // No static path — almost always a dynamic-dispatch break. INSTEAD of
+            // telling the agent to chase the gap with codegraph_node/callers/callees
+            // (which fans out into 3-4 follow-up tool calls + a Read), inline the
+            // material those would have returned right here. Measured on cosmos-Q3:
+            // the failed-trace + subsequent fan-out used to cost ~2× a single
+            // sufficient trace call; this branch closes that gap.
+            // Prefer the path-proximity-best pair we identified above (e.g. gov's
+            // EndBlocker × gov's Tally) over the FTS top-pick (simapp's wrapper).
+            const start = bestPair?.f ?? fromTry[0];
+            const end = bestPair?.t ?? toTry[0];
+            const fileCache = new Map();
             const lines = [
-                `No direct call path from "${from}" to "${to}".`,
+                `No direct static call path from "${from}" to "${to}" — the chain almost certainly breaks at dynamic dispatch (a callback / interface dispatch / framework hook / metaclass). Both endpoint bodies + their immediate neighbors are inlined below; answer from them — a follow-up codegraph_node/callers/callees on these would just return what is already here.`,
                 '',
-                (overCap
-                    ? `(Only a ${overCap.length}-hop indirect chain connects them — almost certainly a BFS wander through unrelated code, not the real flow.) `
-                    : '') +
-                    'The direct chain most likely breaks at **dynamic dispatch** (a callback, descriptor, ' +
-                    'metaclass, or attribute-as-callable) that static parsing cannot resolve into an edge. ' +
-                    `Inspect \`${start.name}\` (${start.filePath}:${start.startLine}) with codegraph_node ` +
-                    '(includeCode=true) — its body usually shows the dynamic call to follow next.',
             ];
-            if (callees.length > 0) {
-                lines.push('', `**${start.name} statically calls:** ${callees.join(', ')}`);
+            if (overCap) {
+                lines.push(`> Indirect chain of ${overCap.length} hops exists but is over the ${MAX_HOPS}-hop cap (usually a BFS wander through unrelated code, not the real execution flow).`, '');
             }
-            return this.textResult(lines.join('\n') + fromMatches.note + toMatches.note);
+            // Track which node IDs we've already inlined a body for so we don't
+            // double-emit when a callee of FROM is also surfaced separately.
+            const inlinedBodies = new Set();
+            const inlineBody = (n, lineCap, charCap) => {
+                if (inlinedBodies.has(n.id))
+                    return false;
+                inlinedBodies.add(n.id);
+                const body = this.sourceRangeAt(cg, n.filePath, n.startLine, n.endLine, fileCache, lineCap, charCap);
+                if (body) {
+                    lines.push(body);
+                    return true;
+                }
+                return false;
+            };
+            const inlineEndpoint = (label, node) => {
+                lines.push(`### ${label}: \`${node.name}\` (${node.filePath}:${node.startLine}-${node.endLine})`);
+                inlineBody(node, 120, 3600);
+                const callers = cg.getCallers(node.id).slice(0, 6);
+                if (callers.length > 0) {
+                    lines.push(`**Callers of \`${node.name}\`:** ` +
+                        callers.map(c => `${c.node.name} (${c.node.filePath}:${c.node.startLine})`).join(', '));
+                }
+                const callees = cg.getCallees(node.id).slice(0, 8);
+                if (callees.length > 0) {
+                    lines.push(`**\`${node.name}\` calls:** ` +
+                        callees.map(c => `${c.node.name} (${c.node.filePath}:${c.node.startLine})`).join(', '));
+                }
+                lines.push('');
+            };
+            inlineEndpoint('FROM', start);
+            if (end.id !== start.id)
+                inlineEndpoint('TO', end);
+            // Inline the OTHER top-level functions/methods in TO's file — that's
+            // where the missing dynamic-dispatch flow usually lives. Concrete
+            // measurement from cosmos-Q1: `msgServer.Send` statically calls only
+            // utility functions (`StringToBytes`, `Wrapf`); its real next-hop
+            // `SendCoins` is invoked via an embedded-interface call (`k.Keeper.SendCoins`)
+            // that static parsing CAN'T see. The flow IS in the same file as the
+            // destination (`x/bank/keeper/send.go`: SendCoins → subUnlockedCoins →
+            // addCoins → setBalance). Pre-inlining those file-mates is what
+            // replaces the agent's "trace fail → search SendCoins → node SendCoins
+            // → trace again" fan-out.
+            const NEIGHBOR_LINES = 40;
+            const NEIGHBOR_CHARS = 1200;
+            const NEIGHBOR_K = 5;
+            const fileSiblings = (anchor) => {
+                // Functions and methods in the same file as the anchor, excluding
+                // the anchor itself and anything we've already inlined. Sort by
+                // distance from the anchor's startLine so the closest symbols come
+                // first (the flow is usually adjacent in the file).
+                const sameFile = cg
+                    .getNodesByKind('function')
+                    .filter((n) => n.filePath === anchor.filePath)
+                    .concat(cg.getNodesByKind('method').filter((n) => n.filePath === anchor.filePath));
+                return sameFile
+                    .filter((n) => n.id !== anchor.id && !inlinedBodies.has(n.id))
+                    .sort((a, b) => Math.abs(a.startLine - anchor.startLine) - Math.abs(b.startLine - anchor.startLine))
+                    .slice(0, NEIGHBOR_K);
+            };
+            const renderSiblings = (label, siblings) => {
+                if (siblings.length === 0)
+                    return;
+                lines.push(`### ${label}`);
+                for (const sib of siblings) {
+                    lines.push('');
+                    lines.push(`- \`${sib.name}\` (${sib.filePath}:${sib.startLine}-${sib.endLine})`);
+                    inlineBody(sib, NEIGHBOR_LINES, NEIGHBOR_CHARS);
+                }
+                lines.push('');
+            };
+            renderSiblings(`Other functions in \`${end.filePath}\` (the flow that the dynamic-dispatch hop reaches — bodies inlined)`, fileSiblings(end));
+            lines.push('> Endpoint bodies + the other functions in the destination\'s file are inlined above. Together they typically cover the missing dynamic-dispatch boundary (interface-method calls like `k.Keeper.SendCoins` that static parsing can\'t follow). **No further codegraph_node / codegraph_callers / codegraph_callees / Read / Grep is needed for any symbol already shown here** — call them again only if you need to walk DEEPER than what is inlined.');
+            return this.textResult(this.truncateOutput(lines.join('\n') + fromMatches.note + toMatches.note));
         }
         const lines = [
             `## Trace: ${from} → ${to}`,
@@ -1591,9 +2021,46 @@ class ToolHandler {
             fileGroups.set(node.filePath, group);
         }
         // Only include files that have entry points or nodes directly connected to entry points
-        const relevantFiles = [...fileGroups.entries()].filter(([, group]) => group.score >= 3);
+        let relevantFiles = [...fileGroups.entries()].filter(([, group]) => group.score >= 3);
         // Extract query terms for relevance checking
         const queryTerms = query.toLowerCase().split(/\s+/).filter(t => t.length >= 3);
+        // Test/spec/icon/i18n file detector — used both for the pre-sort hard
+        // filter (tiny tier) and the comparator deprioritization (all tiers).
+        const isLowValue = (p) => {
+            const lp = p.toLowerCase();
+            return (/\/(tests?|__tests?__|spec)\//.test(lp) ||
+                /_test\.go$/.test(lp) ||
+                /(?:^|\/)test_[^/]+\.py$/.test(lp) ||
+                /_test\.py$/.test(lp) ||
+                /_spec\.rb$/.test(lp) ||
+                /_test\.rb$/.test(lp) ||
+                /\.(test|spec)\.[jt]sx?$/.test(lp) ||
+                /(test|spec|tests)\.(java|kt|scala)$/.test(lp) ||
+                /(tests?|spec)\.cs$/.test(lp) ||
+                /tests?\.swift$/.test(lp) ||
+                /_test\.dart$/.test(lp) ||
+                /\bicons?\b/.test(lp) ||
+                /\bi18n\b/.test(lp));
+        };
+        // Tiny-tier hard-exclude: on small projects (`excludeLowValueFiles`
+        // budget flag), one slipped test/spec file dominates the per-file budget
+        // (cobra's `command_test.go` displaced `args.go` and contributed ~10KB of
+        // pure noise to "How does cobra parse commands?"). The sort-step
+        // deprioritization isn't enough at small N. Skip the hard-exclude when
+        // the query itself is about tests — that's the legitimate "explore the
+        // tests" case where the agent does want them.
+        if (budget.excludeLowValueFiles) {
+            const queryMentionsTests = /\b(test|tests|testing|spec|verify|verifies)\b/i.test(query);
+            if (!queryMentionsTests) {
+                const nonLow = relevantFiles.filter(([p]) => !isLowValue(p));
+                // Only apply the hard-filter if we still have at least 2 non-test
+                // candidates after the cut — otherwise the agent is asking about an
+                // area where tests are the only signal, and we should not strip them.
+                if (nonLow.length >= 2) {
+                    relevantFiles = nonLow;
+                }
+            }
+        }
         // Sort files: highest relevance first, deprioritize low-value files
         const sortedFiles = relevantFiles.sort((a, b) => {
             const aPath = a[0].toLowerCase();
@@ -1609,14 +2076,20 @@ class ToolHandler {
             const bRelevant = hasQueryRelevance(bPath, b[1].nodes);
             if (aRelevant !== bRelevant)
                 return aRelevant ? -1 : 1;
-            // Deprioritize test files, icon files, and i18n files
-            const isLowValue = (p) => /\/(tests?|__tests?__|spec)\//i.test(p) ||
-                /\bicons?\b/i.test(p) ||
-                /\bi18n\b/i.test(p);
             const aLow = isLowValue(aPath);
             const bLow = isLowValue(bPath);
             if (aLow !== bLow)
                 return aLow ? 1 : -1;
+            // Deprioritize generated source (.pb.go / .pulsar.go / _mocks.go / …) —
+            // the agent rarely needs to see the protobuf scaffold or gomock output
+            // when asking about the actual flow, and dumping their bodies inflates
+            // the response (the cosmos Q3 explore otherwise leads with
+            // `expected_keepers_mocks.go`, displacing the real `tally.go` content
+            // and forcing the agent to Read tally.go anyway).
+            const aGen = (0, generated_detection_1.isGeneratedFile)(a[0]);
+            const bGen = (0, generated_detection_1.isGeneratedFile)(b[0]);
+            if (aGen !== bGen)
+                return aGen ? 1 : -1;
             if (a[1].score !== b[1].score)
                 return b[1].score - a[1].score;
             return b[1].nodes.length - a[1].nodes.length;
@@ -2149,9 +2622,20 @@ class ToolHandler {
         if (allFiles.length === 0) {
             return this.textResult('No files indexed. Run `codegraph index` first.');
         }
-        // Filter by path prefix
-        let files = pathFilter
-            ? allFiles.filter(f => f.path.startsWith(pathFilter) || f.path.startsWith('./' + pathFilter))
+        // Filter by path prefix. Stored paths are project-relative POSIX (e.g.
+        // "src/foo.ts"), but agents commonly pass project-root variants like "/",
+        // ".", "./", "" or Windows-style "src\foo" — and prefixes with leading
+        // "/", "./" or "\". Normalize all of those before matching so the agent
+        // gets results instead of falling back to Read/Glob (see #426).
+        const normalizedFilter = pathFilter
+            ? pathFilter
+                .replace(/\\/g, '/')
+                .replace(/^(?:\.?\/+)+/, '')
+                .replace(/^\.$/, '')
+                .replace(/\/+$/, '')
+            : '';
+        let files = normalizedFilter
+            ? allFiles.filter(f => f.path === normalizedFilter || f.path.startsWith(normalizedFilter + '/'))
             : allFiles;
         // Filter by glob pattern
         if (pattern) {
@@ -2369,10 +2853,19 @@ class ToolHandler {
             return { node: exactMatches[0].node, note: '' };
         }
         if (exactMatches.length > 1) {
+            // Down-rank generated files (.pb.go, .pulsar.go, _grpc.pb.go, …)
+            // so a query like "Send" prefers the keeper implementation over
+            // the protobuf-generated interface stub. Stable sort preserves
+            // FTS order within each group. See generated-detection.ts.
+            const ranked = [...exactMatches].sort((a, b) => {
+                const aGen = (0, generated_detection_1.isGeneratedFile)(a.node.filePath) ? 1 : 0;
+                const bGen = (0, generated_detection_1.isGeneratedFile)(b.node.filePath) ? 1 : 0;
+                return aGen - bGen;
+            });
             // Multiple exact matches - pick first, note the others
-            const picked = exactMatches[0].node;
-            const others = exactMatches.slice(1).map(r => `${r.node.name} (${r.node.kind}) at ${r.node.filePath}:${r.node.startLine}`);
-            const note = `\n\n> **Note:** ${exactMatches.length} symbols named "${symbol}". Showing results for \`${picked.filePath}:${picked.startLine}\`. Others: ${others.join(', ')}`;
+            const picked = ranked[0].node;
+            const others = ranked.slice(1).map(r => `${r.node.name} (${r.node.kind}) at ${r.node.filePath}:${r.node.startLine}`);
+            const note = `\n\n> **Note:** ${ranked.length} symbols named "${symbol}". Showing results for \`${picked.filePath}:${picked.startLine}\`. Others: ${others.join(', ')}`;
             return { node: picked, note };
         }
         // No exact match. For qualified lookups, don't silently fall back
@@ -2405,9 +2898,17 @@ class ToolHandler {
             const node = exactMatches[0]?.node ?? results[0].node;
             return { nodes: [node], note: '' };
         }
-        const locations = exactMatches.map(r => `${r.node.kind} at ${r.node.filePath}:${r.node.startLine}`);
-        const note = `\n\n> **Note:** Aggregated results across ${exactMatches.length} symbols named "${symbol}": ${locations.join(', ')}`;
-        return { nodes: exactMatches.map(r => r.node), note };
+        // Same generated-file down-rank as findSymbol — keeps callers/callees
+        // /impact aggregation aligned (a query against "Send" returns the
+        // hand-written implementations before the protobuf scaffold).
+        const ranked = [...exactMatches].sort((a, b) => {
+            const aGen = (0, generated_detection_1.isGeneratedFile)(a.node.filePath) ? 1 : 0;
+            const bGen = (0, generated_detection_1.isGeneratedFile)(b.node.filePath) ? 1 : 0;
+            return aGen - bGen;
+        });
+        const locations = ranked.map(r => `${r.node.kind} at ${r.node.filePath}:${r.node.startLine}`);
+        const note = `\n\n> **Note:** Aggregated results across ${ranked.length} symbols named "${symbol}": ${locations.join(', ')}`;
+        return { nodes: ranked.map(r => r.node), note };
     }
     /**
      * Truncate output if it exceeds the maximum length