@stupidloud/codegraph 0.7.14 → 0.7.20

package/dist/mcp/tools.js

@@ -40,6 +40,7 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ToolHandler = exports.tools = void 0;
 exports.getExploreBudget = getExploreBudget;
+exports.getExploreOutputBudget = getExploreOutputBudget;
 const index_1 = __importStar(require("../index"));
 const crypto_1 = require("crypto");
 const fs_1 = require("fs");
@@ -49,6 +50,19 @@ const path_1 = require("path");
 const db_1 = require("../db");
 /** Maximum output length to prevent context bloat (characters) */
 const MAX_OUTPUT_LENGTH = 15000;
+/**
+ * Rust path roots that have no file-system equivalent — `crate` is the
+ * current crate, `super` is the parent module, `self` is the current
+ * module. Used by `matchesSymbol` to strip these before file-path
+ * matching so `crate::configurator::stage_apply::run` resolves the
+ * same as `configurator::stage_apply::run`.
+ */
+const RUST_PATH_PREFIXES = new Set(['crate', 'super', 'self']);
+/** Last `::` / `.` / `/`-separated segment of a qualified symbol. */
+function lastQualifierPart(symbol) {
+    const parts = symbol.split(/::|[./]/).filter((p) => p.length > 0);
+    return parts[parts.length - 1] ?? symbol;
+}
 /**
  * Calculate the recommended number of codegraph_explore calls based on project size.
  * Larger codebases need more exploration calls to cover their surface area,
@@ -65,6 +79,92 @@ function getExploreBudget(fileCount) {
         return 4;
     return 5;
 }
+function getExploreOutputBudget(fileCount) {
+    if (fileCount < 500) {
+        return {
+            maxOutputChars: 18000,
+            defaultMaxFiles: 5,
+            maxCharsPerFile: 3800,
+            gapThreshold: 8,
+            maxSymbolsInFileHeader: 6,
+            maxEdgesPerRelationshipKind: 6,
+            includeRelationships: true,
+            includeAdditionalFiles: false,
+            includeCompletenessSignal: false,
+            includeBudgetNote: false,
+        };
+    }
+    if (fileCount < 5000) {
+        return {
+            maxOutputChars: 28000,
+            defaultMaxFiles: 9,
+            maxCharsPerFile: 5000,
+            gapThreshold: 12,
+            maxSymbolsInFileHeader: 10,
+            maxEdgesPerRelationshipKind: 10,
+            includeRelationships: true,
+            includeAdditionalFiles: true,
+            includeCompletenessSignal: true,
+            includeBudgetNote: true,
+        };
+    }
+    if (fileCount < 15000) {
+        return {
+            maxOutputChars: 35000,
+            defaultMaxFiles: 12,
+            maxCharsPerFile: 7000,
+            gapThreshold: 15,
+            maxSymbolsInFileHeader: 15,
+            maxEdgesPerRelationshipKind: 15,
+            includeRelationships: true,
+            includeAdditionalFiles: true,
+            includeCompletenessSignal: true,
+            includeBudgetNote: true,
+        };
+    }
+    return {
+        maxOutputChars: 38000,
+        defaultMaxFiles: 14,
+        maxCharsPerFile: 7000,
+        gapThreshold: 15,
+        maxSymbolsInFileHeader: 15,
+        maxEdgesPerRelationshipKind: 15,
+        includeRelationships: true,
+        includeAdditionalFiles: true,
+        includeCompletenessSignal: true,
+        includeBudgetNote: true,
+    };
+}
+/**
+ * Whether `codegraph_explore` should prefix source lines with their line
+ * numbers (cat -n style: `<num>\t<code>`).
+ *
+ * Line numbers let the agent cite `file:line` straight from the explore
+ * payload instead of re-Reading the file just to find a line number — the
+ * dominant residual cost on precise-tracing questions (#185 follow-up).
+ *
+ * Defaults ON. Set `CODEGRAPH_EXPLORE_LINENUMS=0` to disable (used by the
+ * A/B harness to measure the payload-cost vs. read-savings tradeoff).
+ */
+function exploreLineNumbersEnabled() {
+    return process.env.CODEGRAPH_EXPLORE_LINENUMS !== '0';
+}
+/**
+ * Prefix each line of a source slice with its 1-based line number, matching
+ * the Read tool's `cat -n` convention (number + tab) so the agent treats it
+ * the same way it treats Read output.
+ *
+ * @param slice  contiguous source text (already extracted from the file)
+ * @param firstLineNumber  the 1-based line number of the slice's first line
+ */
+function numberSourceLines(slice, firstLineNumber) {
+    const out = [];
+    const split = slice.split('\n');
+    for (let i = 0; i < split.length; i++) {
+        out.push(`${firstLineNumber + i}\t${split[i]}`);
+    }
+    return out.join('\n');
+}
 /**
  * Mark a Claude session as having consulted MCP tools.
  * This enables Grep/Glob/Bash commands that would otherwise be blocked.
@@ -97,7 +197,7 @@ const projectPathProperty = {
 exports.tools = [
     {
         name: 'codegraph_search',
-        description: 'Quick symbol search by name. Returns locations only (no code). Use codegraph_context instead for comprehensive task context.',
+        description: 'Quick symbol search by name. Returns locations only (no code) — best for pinpoint "where is X defined / find the symbol named X" lookups. For understanding how something works or tracing a flow, lead with codegraph_explore instead of searching then reading.',
         inputSchema: {
             type: 'object',
             properties: {
@@ -227,13 +327,13 @@ exports.tools = [
     },
     {
         name: 'codegraph_explore',
-        description: 'Deep exploration tool — returns comprehensive context for a topic in a SINGLE call. Groups all relevant source code by file (contiguous sections, not snippets), includes a relationship map, and uses deeper graph traversal. Designed to replace multiple codegraph_node + file Read calls. Use this instead of codegraph_context when you need thorough understanding. IMPORTANT: Use specific symbol names, file names, or short code terms in your query — NOT natural language sentences. Before calling this, use codegraph_search to discover relevant symbol names, then include those names in your query. Bad: "how are agent prompts loaded and passed to the CLI". Good: "readAgentsFromDirectory createClaudeSession chat-manager agents.ts".',
+        description: 'PRIMARY TOOL for understanding questions — "how does X work", "trace X end to end", "explain the Y system", architecture/onboarding. Returns comprehensive context in a SINGLE call: relevant source grouped by file (contiguous, line-numbered sections, not snippets) + a relationship map + deep graph traversal. It REPLACES the grep+Read exploration loop: feed it the key symbol/file names and read its output — do NOT Read the files one by one. It works best when your query names the relevant symbols (e.g. "readAgentsFromDirectory createClaudeSession chat-manager agents.ts"); if the question is a plain sentence that names nothing concrete, do ONE quick codegraph_search or codegraph_context to surface the names, then call this with them. After exploring, use codegraph_node / Read only to fill specific gaps it did not cover. Prefer codegraph_search over this only for a pinpoint "where is X defined" lookup.',
         inputSchema: {
             type: 'object',
             properties: {
                 query: {
                     type: 'string',
-                    description: 'Symbol names, file names, or short code terms to explore (e.g., "AuthService loginUser session-manager", "GraphTraverser BFS impact traversal.ts"). Use codegraph_search first to find relevant names.',
+                    description: 'What to explore. A short list of symbol/file/keyword terms works best (e.g., "AuthService loginUser session-manager", "GraphTraverser BFS impact traversal.ts"), but a plain-language phrase also works — the tool runs its own retrieval. No need to codegraph_search first.',
                 },
                 maxFiles: {
                     type: 'number',
@@ -606,22 +706,34 @@ class ToolHandler {
         const formatted = this.formatImpact(symbol, mergedImpact) + allMatches.note;
         return this.textResult(this.truncateOutput(formatted));
     }
-    /** Maximum output for explore tool — sized to stay under MCP client token limits (~10k tokens) */
-    static EXPLORE_MAX_OUTPUT = 35000;
     /**
      * Handle codegraph_explore — deep exploration in a single call
      *
      * Strategy: find relevant symbols via graph traversal, group by file,
      * then read contiguous file sections covering all symbols per file.
      * This replaces multiple codegraph_node + Read calls.
+     *
+     * Output size is adaptive to project file count via
+     * `getExploreOutputBudget` — see #185 for why a fixed 35k cap was a
+     * tax on small projects while earning its keep on large ones.
      */
     async handleExplore(args) {
         const query = this.validateString(args.query, 'query');
         if (typeof query !== 'string')
             return query;
         const cg = this.getCodeGraph(args.projectPath);
-        const maxFiles = (0, utils_1.clamp)(args.maxFiles || 12, 1, 20);
         const projectRoot = cg.getProjectRoot();
+        // Resolve adaptive output budget from project size. Falls back to the
+        // largest-tier defaults if stats aren't available, which preserves
+        // pre-#185 behavior for callers that hit the rare stats failure.
+        let budget;
+        try {
+            budget = getExploreOutputBudget(cg.getStats().fileCount);
+        }
+        catch {
+            budget = getExploreOutputBudget(Infinity);
+        }
+        const maxFiles = (0, utils_1.clamp)(args.maxFiles || budget.defaultMaxFiles, 1, 20);
         // Step 1: Find relevant context with generous parameters.
         // Use a large maxNodes budget — explore has its own 35k char output limit
         // that prevents context bloat, so more nodes just means better coverage
@@ -705,7 +817,7 @@ class ToolHandler {
         // Relationship map — show how symbols connect
         const significantEdges = subgraph.edges.filter(e => e.kind !== 'contains' // skip contains — it's implied by file grouping
         );
-        if (significantEdges.length > 0) {
+        if (budget.includeRelationships && significantEdges.length > 0) {
             lines.push('### Relationships');
             lines.push('');
             // Group edges by kind for readability
@@ -720,14 +832,14 @@ class ToolHandler {
                 byKind.set(edge.kind, group);
             }
             for (const [kind, edges] of byKind) {
-                // Show up to 15 relationships per kind
-                const shown = edges.slice(0, 15);
+                const cap = budget.maxEdgesPerRelationshipKind;
+                const shown = edges.slice(0, cap);
                 lines.push(`**${kind}:**`);
                 for (const e of shown) {
                     lines.push(`- ${e.source} → ${e.target}`);
                 }
-                if (edges.length > 15) {
-                    lines.push(`- ... and ${edges.length - 15} more`);
+                if (edges.length > cap) {
+                    lines.push(`- ... and ${edges.length - cap} more`);
                 }
                 lines.push('');
             }
@@ -737,10 +849,11 @@ class ToolHandler {
         lines.push('');
         let totalChars = lines.join('\n').length;
         let filesIncluded = 0;
+        let anyFileTrimmed = false;
         for (const [filePath, group] of sortedFiles) {
             if (filesIncluded >= maxFiles)
                 break;
-            if (totalChars > ToolHandler.EXPLORE_MAX_OUTPUT * 0.9)
+            if (totalChars > budget.maxOutputChars * 0.9)
                 break;
             const absPath = (0, utils_1.validatePathWithinRoot)(projectRoot, filePath);
             if (!absPath || !(0, fs_1.existsSync)(absPath))
@@ -755,14 +868,37 @@ class ToolHandler {
             const fileLines = fileContent.split('\n');
             const lang = group.nodes[0]?.language || '';
             // Cluster nearby symbols to avoid reading huge gaps between distant symbols.
-            // Sort by start line, then merge overlapping/adjacent ranges (within 15 lines).
-            // Include both node ranges AND edge source locations so template sections
-            // with component usages/calls are covered (not just script block symbols).
+            // Sort by start line, then merge overlapping/adjacent ranges (within the
+            // adaptive gap threshold). Include both node ranges AND edge source
+            // locations so template sections with component usages/calls are
+            // covered (not just script block symbols).
+            //
+            // Each range carries an `importance` score so we can rank clusters
+            // when the per-file budget forces us to drop some: entry-point nodes
+            // are worth 10, directly-connected nodes 3, peripheral nodes 1, and
+            // bare edge-source lines 2 (less than a connected node but more than
+            // a peripheral one — they hint at a reference but aren't a definition).
+            // Container kinds whose body can span most/all of a file. When such a
+            // node covers most of the file we drop it from the ranges: keeping it
+            // would merge every method inside it into one giant cluster spanning
+            // the whole file, which then tail-trims down to just the container's
+            // opening lines (its header/declarations) and buries the methods the
+            // query actually asked about (#185 follow-up — Session.swift in
+            // Alamofire is the canonical case: the `Session` class spans ~1,400
+            // lines). We want the granular symbols inside, not the envelope.
+            const ENVELOPE_KINDS = new Set(['file', 'module', 'class', 'struct', 'interface', 'enum', 'namespace', 'protocol', 'trait', 'component']);
             const ranges = group.nodes
                 .filter(n => n.startLine > 0 && n.endLine > 0)
-                // Skip file/component nodes that span the entire file — they'd create one giant cluster
-                .filter(n => !(n.kind === 'component' && n.startLine === 1 && n.endLine >= fileLines.length - 1))
-                .map(n => ({ start: n.startLine, end: n.endLine, name: n.name, kind: n.kind }));
+                // Drop whole-file envelope nodes (containers covering >50% of the file).
+                .filter(n => !(ENVELOPE_KINDS.has(n.kind) && (n.endLine - n.startLine + 1) > fileLines.length * 0.5))
+                .map(n => {
+                let importance = 1;
+                if (entryNodeIds.has(n.id))
+                    importance = 10;
+                else if (connectedToEntry.has(n.id))
+                    importance = 3;
+                return { start: n.startLine, end: n.endLine, name: n.name, kind: n.kind, importance };
+            });
             // Add edge source locations in this file — captures template references
             // (component usages, event handlers) that aren't nodes themselves.
             // Query edges directly from the DB (not just the subgraph) because BFS
@@ -780,48 +916,148 @@ class ToolHandler {
                     // Look up target name from subgraph first, fall back to edge kind
                     const targetNode = subgraph.nodes.get(edge.target);
                     const targetName = targetNode?.name ?? edge.kind;
-                    ranges.push({ start: edge.line, end: edge.line, name: targetName, kind: edge.kind });
+                    ranges.push({ start: edge.line, end: edge.line, name: targetName, kind: edge.kind, importance: 2 });
                 }
             }
             ranges.sort((a, b) => a.start - b.start);
             if (ranges.length === 0)
                 continue;
-            const GAP_THRESHOLD = 15; // merge sections within 15 lines of each other
+            const gapThreshold = budget.gapThreshold;
             const clusters = [];
-            let current = { start: ranges[0].start, end: ranges[0].end, symbols: [`${ranges[0].name}(${ranges[0].kind})`] };
+            let current = {
+                start: ranges[0].start,
+                end: ranges[0].end,
+                symbols: [`${ranges[0].name}(${ranges[0].kind})`],
+                score: ranges[0].importance,
+                maxImportance: ranges[0].importance,
+            };
             for (let i = 1; i < ranges.length; i++) {
                 const r = ranges[i];
-                if (r.start <= current.end + GAP_THRESHOLD) {
+                if (r.start <= current.end + gapThreshold) {
                     current.end = Math.max(current.end, r.end);
                     current.symbols.push(`${r.name}(${r.kind})`);
+                    current.score += r.importance;
+                    current.maxImportance = Math.max(current.maxImportance, r.importance);
                 }
                 else {
                     clusters.push(current);
-                    current = { start: r.start, end: r.end, symbols: [`${r.name}(${r.kind})`] };
+                    current = {
+                        start: r.start,
+                        end: r.end,
+                        symbols: [`${r.name}(${r.kind})`],
+                        score: r.importance,
+                        maxImportance: r.importance,
+                    };
                 }
             }
             clusters.push(current);
-            // Build file section output from clusters
+            // Build file section output from clusters, capped by per-file budget.
+            // The pathological case (#185): a file like Session.swift where every
+            // method is adjacent collapses into one cluster spanning the whole
+            // file, and dumping that into the agent's context is most of the
+            // token cost on small projects. We pick clusters in priority order
+            // until the per-file char cap is hit. Truly enormous single clusters
+            // get tail-trimmed with a marker.
             const contextPadding = 3;
+            const withLineNumbers = exploreLineNumbersEnabled();
+            const buildSection = (c) => {
+                const startIdx = Math.max(0, c.start - 1 - contextPadding);
+                const endIdx = Math.min(fileLines.length, c.end + contextPadding);
+                const slice = fileLines.slice(startIdx, endIdx).join('\n');
+                // startIdx is 0-based, so the slice's first line is line startIdx + 1.
+                return withLineNumbers ? numberSourceLines(slice, startIdx + 1) : slice;
+            };
+            // Language-neutral separator (no `//` — not a comment in Python, Ruby,
+            // etc.). With line numbers on, the line-number jump also signals the gap.
+            const GAP_MARKER = '\n\n... (gap) ...\n\n';
+            // Rank clusters for inclusion under the per-file cap. Entry-point
+            // clusters come first: a cluster containing a query entry point
+            // (importance 10) must outrank a dense block of mere declarations,
+            // otherwise on a large file like Session.swift the top-of-file class
+            // header + property list (many adjacent low-importance nodes, high
+            // density) wins the budget and buries the actual methods the query
+            // asked about (perform/didCreateURLRequest/task live deep in the
+            // file). Within the same importance tier, prefer density (score per
+            // line) so we still favor focused clusters over sprawling ones, then
+            // smaller span as a cheap-to-include tiebreak.
+            const rankedClusters = clusters
+                .map((c, i) => ({ idx: i, span: c.end - c.start + 1, c }))
+                .sort((a, b) => {
+                if (b.c.maxImportance !== a.c.maxImportance)
+                    return b.c.maxImportance - a.c.maxImportance;
+                const densityA = a.c.score / a.span;
+                const densityB = b.c.score / b.span;
+                if (densityB !== densityA)
+                    return densityB - densityA;
+                if (b.c.score !== a.c.score)
+                    return b.c.score - a.c.score;
+                return a.span - b.span;
+            });
+            const chosenIndices = new Set();
+            let projectedChars = 0;
+            for (const rc of rankedClusters) {
+                const sectionLen = buildSection(rc.c).length + (chosenIndices.size > 0 ? GAP_MARKER.length : 0);
+                // Always take the top-ranked cluster, even if oversize, so we don't
+                // return an empty file section (agent would then re-Read the file,
+                // negating the savings).
+                if (chosenIndices.size === 0) {
+                    chosenIndices.add(rc.idx);
+                    projectedChars += sectionLen;
+                    continue;
+                }
+                if (projectedChars + sectionLen > budget.maxCharsPerFile)
+                    continue;
+                chosenIndices.add(rc.idx);
+                projectedChars += sectionLen;
+            }
+            // Emit chosen clusters in source order so the file reads top-to-bottom.
             let fileSection = '';
             const allSymbols = [];
-            for (const cluster of clusters) {
-                const startIdx = Math.max(0, cluster.start - 1 - contextPadding);
-                const endIdx = Math.min(fileLines.length, cluster.end + contextPadding);
-                const section = fileLines.slice(startIdx, endIdx).join('\n');
-                if (fileSection.length > 0) {
-                    fileSection += '\n\n// ... (gap) ...\n\n';
-                }
+            let fileTrimmed = false;
+            for (let i = 0; i < clusters.length; i++) {
+                if (!chosenIndices.has(i))
+                    continue;
+                const cluster = clusters[i];
+                const section = buildSection(cluster);
+                if (fileSection.length > 0)
+                    fileSection += GAP_MARKER;
                 fileSection += section;
                 allSymbols.push(...cluster.symbols);
             }
-            // Skip if this section would blow the output limit
-            if (totalChars + fileSection.length + 200 > ToolHandler.EXPLORE_MAX_OUTPUT) {
-                const budget = ToolHandler.EXPLORE_MAX_OUTPUT - totalChars - 200;
-                if (budget < 500)
+            // If a single chosen cluster is still oversize (long monolithic
+            // function), tail-trim it. Better one trimmed view than nothing.
+            if (fileSection.length > budget.maxCharsPerFile) {
+                fileSection = fileSection.slice(0, budget.maxCharsPerFile) + '\n... (trimmed) ...';
+                fileTrimmed = true;
+            }
+            if (chosenIndices.size < clusters.length || fileTrimmed) {
+                anyFileTrimmed = true;
+            }
+            // Dedupe + cap the symbols list shown in the per-file header. Some
+            // files (Session.swift in Alamofire) produced 3.4KB symbol lists
+            // from cluster scoring + edge-source lines, dwarfing the per-file
+            // body cap. Show top names by frequency, with a "+N more" tail.
+            const symbolCounts = new Map();
+            for (const s of allSymbols) {
+                symbolCounts.set(s, (symbolCounts.get(s) ?? 0) + 1);
+            }
+            const sortedSymbols = [...symbolCounts.entries()]
+                .sort((a, b) => b[1] - a[1])
+                .map(([name]) => name);
+            const headerCap = budget.maxSymbolsInFileHeader;
+            const headerSymbols = sortedSymbols.slice(0, headerCap);
+            const omittedCount = sortedSymbols.length - headerSymbols.length;
+            const headerSuffix = omittedCount > 0
+                ? `${headerSymbols.join(', ')}, +${omittedCount} more`
+                : headerSymbols.join(', ');
+            const fileHeader = `#### ${filePath} — ${headerSuffix}`;
+            // Respect the total output cap on a file-by-file basis.
+            if (totalChars + fileSection.length + 200 > budget.maxOutputChars) {
+                const remaining = budget.maxOutputChars - totalChars - 200;
+                if (remaining < 500)
                     break;
-                const trimmed = fileSection.slice(0, budget) + '\n// ... trimmed ...';
-                lines.push(`#### ${filePath} — ${allSymbols.join(', ')}`);
+                const trimmed = fileSection.slice(0, remaining) + '\n... (trimmed) ...';
+                lines.push(fileHeader);
                 lines.push('');
                 lines.push('```' + lang);
                 lines.push(trimmed);
@@ -829,9 +1065,10 @@ class ToolHandler {
                 lines.push('');
                 totalChars += trimmed.length + 200;
                 filesIncluded++;
+                anyFileTrimmed = true;
                 break;
             }
-            lines.push(`#### ${filePath} — ${allSymbols.join(', ')}`);
+            lines.push(fileHeader);
             lines.push('');
             lines.push('```' + lang);
             lines.push(fileSection);
@@ -840,36 +1077,51 @@ class ToolHandler {
             totalChars += fileSection.length + 200;
             filesIncluded++;
         }
-        // Add remaining files as references (from both relevant and peripheral files)
-        const remainingRelevant = sortedFiles.slice(filesIncluded);
-        const peripheralFiles = [...fileGroups.entries()]
-            .filter(([, group]) => group.score < 3)
-            .sort((a, b) => b[1].score - a[1].score);
-        const remainingFiles = [...remainingRelevant, ...peripheralFiles];
-        if (remainingFiles.length > 0) {
-            lines.push('### Additional relevant files (not shown)');
-            lines.push('');
-            for (const [filePath, group] of remainingFiles.slice(0, 10)) {
-                const symbols = group.nodes.map(n => `${n.name}:${n.startLine}`).join(', ');
-                lines.push(`- ${filePath}: ${symbols}`);
-            }
-            if (remainingFiles.length > 10) {
-                lines.push(`- ... and ${remainingFiles.length - 10} more files`);
+        // Add remaining files as references (from both relevant and peripheral files).
+        // Small projects (per budget) skip this — the relevant story already fits
+        // in the source section, and a trailing pointer list is pure overhead.
+        if (budget.includeAdditionalFiles) {
+            const remainingRelevant = sortedFiles.slice(filesIncluded);
+            const peripheralFiles = [...fileGroups.entries()]
+                .filter(([, group]) => group.score < 3)
+                .sort((a, b) => b[1].score - a[1].score);
+            const remainingFiles = [...remainingRelevant, ...peripheralFiles];
+            if (remainingFiles.length > 0) {
+                lines.push('### Additional relevant files (not shown)');
+                lines.push('');
+                for (const [filePath, group] of remainingFiles.slice(0, 10)) {
+                    const symbols = group.nodes.map(n => `${n.name}:${n.startLine}`).join(', ');
+                    lines.push(`- ${filePath}: ${symbols}`);
+                }
+                if (remainingFiles.length > 10) {
+                    lines.push(`- ... and ${remainingFiles.length - 10} more files`);
+                }
             }
         }
-        // Add completeness signal so agents know they don't need to re-read these files
-        lines.push('');
-        lines.push('---');
-        lines.push(`> **Complete source code is included above for ${filesIncluded} files.** You do NOT need to re-read these files — the relevant sections are already shown in full. Only use Read/Grep for files listed under "Additional relevant files" if you need more detail.`);
-        // Add explore budget note based on project size
-        try {
-            const stats = cg.getStats();
-            const budget = getExploreBudget(stats.fileCount);
+        // Add completeness signal so agents know they don't need to re-read these files.
+        // On small projects the budget gates this off — but if we actually had to
+        // trim or drop clusters, surface a brief note so the agent knows it can
+        // still Read for more detail.
+        if (budget.includeCompletenessSignal) {
             lines.push('');
-            lines.push(`> **Explore budget: ${budget} calls max for this project (${stats.fileCount.toLocaleString()} files indexed).** Stop exploring and synthesize your answer once you've used ${budget} calls — do NOT make additional explore calls beyond this budget.`);
+            lines.push('---');
+            lines.push(`> **Complete source code is included above for ${filesIncluded} files.** You do NOT need to re-read these files — the relevant sections are already shown in full. Only use Read/Grep for files listed under "Additional relevant files" if you need more detail.`);
         }
-        catch {
-            // Stats unavailable — skip budget note
+        else if (anyFileTrimmed) {
+            lines.push('');
+            lines.push(`> Some file sections were trimmed for size. Use \`codegraph_node\` or Read for the full source if needed.`);
+        }
+        // Add explore budget note based on project size
+        if (budget.includeBudgetNote) {
+            try {
+                const stats = cg.getStats();
+                const callBudget = getExploreBudget(stats.fileCount);
+                lines.push('');
+                lines.push(`> **Explore budget: ${callBudget} calls max for this project (${stats.fileCount.toLocaleString()} files indexed).** Stop exploring and synthesize your answer once you've used ${callBudget} calls — do NOT make additional explore calls beyond this budget.`);
+            }
+            catch {
+                // Stats unavailable — skip budget note
+            }
         }
         return this.textResult(lines.join('\n'));
     }
@@ -1092,9 +1344,22 @@ class ToolHandler {
      * Returns the best match and a note about alternatives if any.
      */
     /**
-     * Check if a node matches a symbol query, supporting both simple names and
-     * qualified "Parent.child" notation (e.g., "Session.request" matches a method
-     * named "request" inside a class named "Session").
+     * Check if a node matches a symbol query.
+     *
+     * Accepts simple names (`run`) and three flavors of qualifier:
+     *   - dotted     `Session.request`         (TS/JS/Python)
+     *   - colon-pair `stage_apply::run`        (Rust, C++, Ruby)
+     *   - slash      `configurator/stage_apply` (path-ish)
+     *
+     * Multi-level qualifiers compose: `crate::configurator::stage_apply::run`
+     * works. Rust path prefixes (`crate`, `super`, `self`) are stripped so
+     * the canonical `crate::module::symbol` form resolves.
+     *
+     * Resolution order, last part must always equal `node.name`:
+     *   1. Suffix-match against `qualifiedName` (handles class-scoped methods
+     *      where the extractor builds the qualified name from the AST stack)
+     *   2. File-path containment (handles file-derived modules in Rust/
+     *      Python — `stage_apply::run` matches a `run` in `stage_apply.rs`)
      */
     matchesSymbol(node, symbol) {
         // Simple name match
@@ -1103,20 +1368,50 @@ class ToolHandler {
         // File basename match (e.g., "product-card" matches "product-card.liquid")
         if (node.kind === 'file' && node.name.replace(/\.[^.]+$/, '') === symbol)
             return true;
-        // Qualified name match: "Parent.child" → look for "::Parent::child" in qualified_name
-        if (symbol.includes('.')) {
-            const parts = symbol.split('.');
-            const qualifiedSuffix = parts.join('::');
-            if (node.qualifiedName.includes(qualifiedSuffix))
-                return true;
-        }
-        return false;
+        // Qualified-name lookups: split on any supported separator. `\w` keeps
+        // identifier chars (incl. `_`) intact; everything else is treated as
+        // a separator we tolerate.
+        if (!/[.\/]|::/.test(symbol))
+            return false;
+        const parts = symbol.split(/::|[./]/).filter((p) => p.length > 0);
+        if (parts.length < 2)
+            return false;
+        const lastPart = parts[parts.length - 1];
+        if (node.name !== lastPart)
+            return false;
+        // Stage 1: qualified-name suffix match. The extractor joins the
+        // semantic hierarchy with `::`, so `Session.request` and
+        // `Session::request` both become `Session::request` here.
+        const colonSuffix = parts.join('::');
+        if (node.qualifiedName.includes(colonSuffix))
+            return true;
+        // Stage 2: file-path containment. Rust modules and Python packages
+        // are not in `qualifiedName` — they're encoded in the file path. So
+        // `stage_apply::run` matches a `run` in any file whose path
+        // contains a `stage_apply` segment (with or without an extension).
+        //
+        // Filter out Rust path prefixes that have no file-system equivalent.
+        const containerHints = parts.slice(0, -1).filter((p) => !RUST_PATH_PREFIXES.has(p));
+        if (containerHints.length === 0)
+            return false;
+        const segments = node.filePath.split('/').filter((s) => s.length > 0);
+        return containerHints.every((hint) => segments.some((seg) => seg === hint || seg.replace(/\.[^.]+$/, '') === hint));
     }
     findSymbol(cg, symbol) {
-        // Use higher limit for qualified lookups (e.g., "Session.request") since the
-        // target may rank lower in FTS when there are many partial matches
-        const limit = symbol.includes('.') ? 50 : 10;
-        const results = cg.searchNodes(symbol, { limit });
+        // Use higher limit for qualified lookups (e.g., "Session.request",
+        // "stage_apply::run") since the target may rank lower in FTS when
+        // there are many partial matches across the qualifier parts.
+        const isQualified = /[.\/]|::/.test(symbol);
+        const limit = isQualified ? 50 : 10;
+        let results = cg.searchNodes(symbol, { limit });
+        // FTS strips colons as a special char, so `stage_apply::run` searches
+        // for the literal `stage_applyrun` and finds nothing. Re-search by
+        // the bare last part and let `matchesSymbol` filter by qualifier.
+        if (isQualified && results.length === 0) {
+            const tail = lastQualifierPart(symbol);
+            if (tail && tail !== symbol)
+                results = cg.searchNodes(tail, { limit });
+        }
         if (results.length === 0 || !results[0]) {
             return null;
         }
@@ -1131,7 +1426,12 @@ class ToolHandler {
             const note = `\n\n> **Note:** ${exactMatches.length} symbols named "${symbol}". Showing results for \`${picked.filePath}:${picked.startLine}\`. Others: ${others.join(', ')}`;
             return { node: picked, note };
         }
-        // No exact match, use best fuzzy match
+        // No exact match. For qualified lookups, don't silently fall back
+        // to a fuzzy result — the user typed a specific qualifier, and
+        // resolving `stage_apply::nonexistent_fn` to the unrelated
+        // `stage_apply.rs` file would be actively misleading (#173).
+        if (isQualified)
+            return null;
         return { node: results[0].node, note: '' };
     }
     /**
@@ -1139,7 +1439,15 @@ class ToolHandler {
      * results across all matching symbols (e.g., multiple classes with an `execute` method).
      */
     findAllSymbols(cg, symbol) {
-        const results = cg.searchNodes(symbol, { limit: 50 });
+        let results = cg.searchNodes(symbol, { limit: 50 });
+        // Mirror the fallback in `findSymbol` for qualified queries — FTS
+        // strips colons, so a module-qualified lookup needs a second pass
+        // by the bare last part.
+        if (results.length === 0 && /[.\/]|::/.test(symbol)) {
+            const tail = lastQualifierPart(symbol);
+            if (tail && tail !== symbol)
+                results = cg.searchNodes(tail, { limit: 50 });
+        }
         if (results.length === 0) {
             return { nodes: [], note: '' };
         }