@monoes/monograph 1.2.0 → 1.2.1

package/dist/src/graph/cross-reference.js

@@ -89,4 +89,27 @@ export function crossReferenceDuplicatesAndDeadCode(db) {
         crossCount: crossIds.length,
     };
 }
+/**
+ * Format a CrossReferenceReport as structured text for LLM consumption.
+ */
+export function formatCrossReferenceReport(report) {
+    const lines = [
+        `Cross-reference analysis: dead code × structural duplicates`,
+        `  Dead (unreachable) file nodes : ${report.deadCount}`,
+        `  Duplicated file nodes         : ${report.duplicateCount}`,
+        `  Both dead AND duplicated      : ${report.crossCount}  (highest-confidence safe-delete candidates)`,
+    ];
+    if (report.crossCount === 0) {
+        lines.push('  No cross-referenced candidates found.');
+        return lines.join('\n');
+    }
+    lines.push('');
+    lines.push('Safe-delete candidates:');
+    for (const f of report.findings) {
+        const loc = f.filePath ? `  ${f.filePath}` : `  (no path) ${f.nodeName}`;
+        lines.push(loc);
+        lines.push(`    ${f.description}`);
+    }
+    return lines.join('\n');
+}
 //# sourceMappingURL=cross-reference.js.map

package/dist/src/graph/cross-reference.js.map

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package/dist/src/graph/cycle-detection.d.ts

@@ -3,4 +3,6 @@ export interface CycleGroup {
     length: number;
 }
 export declare function findCycles(fileIds: number[], edges: Map<number, number[]>, idToPath: Map<number, string>, skipTypeOnly?: boolean, typeOnlyEdges?: Set<string>): CycleGroup[];
+/** Format cycle groups as structured text for LLM consumption. */
+export declare function formatCycleGroups(groups: CycleGroup[]): string;
 //# sourceMappingURL=cycle-detection.d.ts.map

package/dist/src/graph/cycle-detection.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cycle-detection.d.ts","sourceRoot":"","sources":["../../../src/graph/cycle-detection.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;CAChB;AAwID,wBAAgB,UAAU,CACxB,OAAO,EAAE,MAAM,EAAE,EACjB,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAC5B,QAAQ,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAC7B,YAAY,UAAQ,EACpB,aAAa,GAAE,GAAG,CAAC,MAAM,CAAa,GACrC,UAAU,EAAE,CAyJd;AAED,kEAAkE;AAClE,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,CAS9D"}

package/dist/src/graph/cycle-detection.js

@@ -10,7 +10,14 @@ function canonicalCycle(cycle, idToPath) {
             minPos = i;
         }
     }
-    return [...cycle.slice(minPos), ...cycle.slice(0, minPos)];
+    if (minPos === 0)
+        return cycle.slice(); // already canonical — single allocation
+    // Single-pass rotation without 3 intermediate arrays (2x slice + spread)
+    const n = cycle.length;
+    const result = new Array(n);
+    for (let i = 0; i < n; i++)
+        result[i] = cycle[(minPos + i) % n];
+    return result;
 }
 function tryRecordCycle(path, idToPath, seen, cycles) {
     const canonical = canonicalCycle(path, idToPath);
@@ -57,7 +64,8 @@ function enumerateElementaryCycles(sccNodes, allSuccs, succRanges, maxCycles, id
     const sccSet = new Set(sccNodes);
     const cycles = [];
     const seen = new Set();
-    const sortedNodes = [...sccNodes].sort((a, b) => {
+    // Use slice() rather than spread to avoid the iterator allocation overhead
+    const sortedNodes = sccNodes.slice().sort((a, b) => {
         const pa = idToPath.get(a) ?? '';
         const pb = idToPath.get(b) ?? '';
         return pa < pb ? -1 : pa > pb ? 1 : 0;
@@ -201,10 +209,25 @@ export function findCycles(fileIds, edges, idToPath, skipTypeOnly = false, typeO
         return pa < pb ? -1 : pa > pb ? 1 : 0;
     });
     return result.map(cycle => ({
-        files: [...cycle]
+        // slice() instead of spread to avoid iterator overhead
+        files: cycle.slice()
             .sort((a, b) => (idToPath.get(a) ?? '').localeCompare(idToPath.get(b) ?? ''))
             .map(id => idToPath.get(id) ?? String(id)),
         length: cycle.length,
     }));
 }
+/** Format cycle groups as structured text for LLM consumption. */
+export function formatCycleGroups(groups) {
+    if (groups.length === 0)
+        return 'No import cycles detected.';
+    const lines = [`Import Cycles (${groups.length} total):`];
+    for (const g of groups.slice(0, 30)) {
+        lines.push(`\n  Cycle (length ${g.length}):`);
+        for (const f of g.files)
+            lines.push(`    ${f}`);
+    }
+    if (groups.length > 30)
+        lines.push(`\n  ... and ${groups.length - 30} more cycles`);
+    return lines.join('\n');
+}
 //# sourceMappingURL=cycle-detection.js.map

package/dist/src/graph/cycle-detection.js.map

@@ -1 +1 @@
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package/dist/src/graph/cycles.d.ts

@@ -1,6 +1,6 @@
 import type { MonographDb } from '../storage/db.js';
 /**
- * Find ALL strongly connected components (SCCs) using Kosaraju's algorithm.
+ * Find ALL strongly connected components (SCCs) using iterative Kosaraju's algorithm.
  *
  * Returns every SCC, including singleton components (single nodes with no self-loop).
  * This is the full SCC decomposition of the graph.
@@ -13,11 +13,19 @@ export declare function findStronglyConnectedComponents(db: MonographDb): string
  * Find all strongly connected components (SCCs) with more than 1 node,
  * or self-loops, and return them as cycle node lists.
  *
- * Uses Kosaraju's algorithm to find SCCs. Each SCC with size > 1 represents
- * a cycle. Self-loops (node -> itself) are also detected separately.
+ * Uses iterative Kosaraju's algorithm to avoid stack overflow on large graphs.
+ * Each SCC with size > 1 represents a cycle. Self-loops are also detected.
  *
  * @param db - The MonographDb instance
  * @returns Array of cycles; each cycle is an array of node ids participating in it.
  */
 export declare function findCycles(db: MonographDb): string[][];
+/**
+ * Format cycle results as structured text with file:line hints for LLM navigation.
+ *
+ * @param cycles - Array of cycle arrays (node ids / file paths)
+ * @param nodeToFile - Optional map from node id to file path for resolving paths
+ * @returns Structured text output suitable for LLM consumption
+ */
+export declare function formatCycles(cycles: string[][], nodeToFile?: Map<string, string>): string;
 //# sourceMappingURL=cycles.d.ts.map

package/dist/src/graph/cycles.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cycles.d.ts","sourceRoot":"","sources":["../../../src/graph/cycles.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAkGpD;;;;;;;;GAQG;AACH,wBAAgB,+BAA+B,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,EAAE,CAsB3E;AAED;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,EAAE,CA+BtD;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,MAAM,EAAE,MAAM,EAAE,EAAE,EAClB,UAAU,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAC/B,MAAM,CAqCR"}

package/dist/src/graph/cycles.js

@@ -1,18 +1,5 @@
-/**
- * Find ALL strongly connected components (SCCs) using Kosaraju's algorithm.
- *
- * Returns every SCC, including singleton components (single nodes with no self-loop).
- * This is the full SCC decomposition of the graph.
- *
- * @param db - The MonographDb instance
- * @returns Array of SCCs; each SCC is an array of node ids in that component.
- */
-export function findStronglyConnectedComponents(db) {
-    const nodeRows = db.prepare('SELECT id FROM nodes').all();
-    const edgeRows = db.prepare('SELECT source_id, target_id FROM edges').all();
-    if (nodeRows.length === 0)
-        return [];
-    const nodes = nodeRows.map(r => r.id);
+/** Build adjacency maps from DB rows (shared by both exports). */
+function buildAdjacency(nodes, edgeRows) {
     const nodeSet = new Set(nodes);
     const adj = new Map();
     const radj = new Map();
@@ -20,43 +7,93 @@ export function findStronglyConnectedComponents(db) {
         adj.set(n, []);
         radj.set(n, []);
     }
+    const selfLoops = new Set();
     for (const { source_id: src, target_id: tgt } of edgeRows) {
         if (!nodeSet.has(src) || !nodeSet.has(tgt))
             continue;
-        if (src === tgt)
+        if (src === tgt) {
+            selfLoops.add(src);
             continue;
+        }
         adj.get(src).push(tgt);
         radj.get(tgt).push(src);
     }
-    const visited = new Set();
-    const finishOrder = [];
-    function dfs1(node) {
-        visited.add(node);
-        for (const neighbor of adj.get(node) ?? []) {
-            if (!visited.has(neighbor))
-                dfs1(neighbor);
+    return { adj, radj, selfLoops };
+}
+/** Iterative DFS pass 1: populate finish order (replaces recursive dfs1). */
+function iterativeDfs1(roots, adj, visited, finishOrder) {
+    for (const root of roots) {
+        if (visited.has(root))
+            continue;
+        // Stack entries: [node, neighborIndex]
+        const stack = [[root, 0]];
+        visited.add(root);
+        while (stack.length > 0) {
+            const frame = stack[stack.length - 1];
+            const [node, idx] = frame;
+            const neighbors = adj.get(node) ?? [];
+            if (idx < neighbors.length) {
+                frame[1]++;
+                const neighbor = neighbors[idx];
+                if (!visited.has(neighbor)) {
+                    visited.add(neighbor);
+                    stack.push([neighbor, 0]);
+                }
+            }
+            else {
+                stack.pop();
+                finishOrder.push(node);
+            }
         }
-        finishOrder.push(node);
-    }
-    for (const node of nodes) {
-        if (!visited.has(node))
-            dfs1(node);
     }
-    const assigned = new Set();
-    const sccs = [];
-    function dfs2(node, component) {
-        assigned.add(node);
+}
+/** Iterative DFS pass 2: collect SCC component (replaces recursive dfs2). */
+function iterativeDfs2(root, radj, assigned, component) {
+    const stack = [root];
+    assigned.add(root);
+    while (stack.length > 0) {
+        const node = stack.pop();
         component.push(node);
         for (const neighbor of radj.get(node) ?? []) {
-            if (!assigned.has(neighbor))
-                dfs2(neighbor, component);
+            if (!assigned.has(neighbor)) {
+                assigned.add(neighbor);
+                stack.push(neighbor);
+            }
         }
     }
+}
+/**
+ * Fetch nodes and edges once and return raw rows (shared helper).
+ */
+function fetchGraphRows(db) {
+    const nodeRows = db.prepare('SELECT id FROM nodes').all();
+    const edgeRows = db.prepare('SELECT source_id, target_id FROM edges').all();
+    return { nodes: nodeRows.map(r => r.id), edgeRows };
+}
+/**
+ * Find ALL strongly connected components (SCCs) using iterative Kosaraju's algorithm.
+ *
+ * Returns every SCC, including singleton components (single nodes with no self-loop).
+ * This is the full SCC decomposition of the graph.
+ *
+ * @param db - The MonographDb instance
+ * @returns Array of SCCs; each SCC is an array of node ids in that component.
+ */
+export function findStronglyConnectedComponents(db) {
+    const { nodes, edgeRows } = fetchGraphRows(db);
+    if (nodes.length === 0)
+        return [];
+    const { adj, radj } = buildAdjacency(nodes, edgeRows);
+    const visited = new Set();
+    const finishOrder = [];
+    iterativeDfs1(nodes, adj, visited, finishOrder);
+    const assigned = new Set();
+    const sccs = [];
     for (let i = finishOrder.length - 1; i >= 0; i--) {
         const node = finishOrder[i];
         if (!assigned.has(node)) {
             const component = [];
-            dfs2(node, component);
+            iterativeDfs2(node, radj, assigned, component);
             sccs.push(component);
         }
     }
@@ -66,68 +103,29 @@ export function findStronglyConnectedComponents(db) {
  * Find all strongly connected components (SCCs) with more than 1 node,
  * or self-loops, and return them as cycle node lists.
  *
- * Uses Kosaraju's algorithm to find SCCs. Each SCC with size > 1 represents
- * a cycle. Self-loops (node -> itself) are also detected separately.
+ * Uses iterative Kosaraju's algorithm to avoid stack overflow on large graphs.
+ * Each SCC with size > 1 represents a cycle. Self-loops are also detected.
  *
  * @param db - The MonographDb instance
  * @returns Array of cycles; each cycle is an array of node ids participating in it.
  */
 export function findCycles(db) {
-    const nodeRows = db.prepare('SELECT id FROM nodes').all();
-    const edgeRows = db.prepare('SELECT source_id, target_id FROM edges').all();
-    if (nodeRows.length === 0)
+    const { nodes, edgeRows } = fetchGraphRows(db);
+    if (nodes.length === 0)
         return [];
-    const nodes = nodeRows.map(r => r.id);
-    const nodeSet = new Set(nodes);
-    // Build adjacency list and reverse adjacency list
-    const adj = new Map();
-    const radj = new Map();
-    for (const n of nodes) {
-        adj.set(n, []);
-        radj.set(n, []);
-    }
-    const selfLoops = new Set();
-    for (const { source_id: src, target_id: tgt } of edgeRows) {
-        if (!nodeSet.has(src) || !nodeSet.has(tgt))
-            continue;
-        if (src === tgt) {
-            selfLoops.add(src);
-            continue;
-        }
-        adj.get(src).push(tgt);
-        radj.get(tgt).push(src);
-    }
-    // Kosaraju's algorithm — pass 1: DFS on original graph, build finish order
+    const { adj, radj, selfLoops } = buildAdjacency(nodes, edgeRows);
+    // Pass 1: iterative DFS on original graph, build finish order
     const visited = new Set();
     const finishOrder = [];
-    function dfs1(node) {
-        visited.add(node);
-        for (const neighbor of adj.get(node) ?? []) {
-            if (!visited.has(neighbor))
-                dfs1(neighbor);
-        }
-        finishOrder.push(node);
-    }
-    for (const node of nodes) {
-        if (!visited.has(node))
-            dfs1(node);
-    }
-    // Kosaraju's algorithm — pass 2: DFS on reverse graph in reverse finish order
+    iterativeDfs1(nodes, adj, visited, finishOrder);
+    // Pass 2: iterative DFS on reverse graph in reverse finish order
     const assigned = new Set();
     const sccs = [];
-    function dfs2(node, component) {
-        assigned.add(node);
-        component.push(node);
-        for (const neighbor of radj.get(node) ?? []) {
-            if (!assigned.has(neighbor))
-                dfs2(neighbor, component);
-        }
-    }
     for (let i = finishOrder.length - 1; i >= 0; i--) {
         const node = finishOrder[i];
         if (!assigned.has(node)) {
             const component = [];
-            dfs2(node, component);
+            iterativeDfs2(node, radj, assigned, component);
             if (component.length > 1) {
                 sccs.push(component);
             }
@@ -139,4 +137,44 @@ export function findCycles(db) {
     }
     return sccs;
 }
+/**
+ * Format cycle results as structured text with file:line hints for LLM navigation.
+ *
+ * @param cycles - Array of cycle arrays (node ids / file paths)
+ * @param nodeToFile - Optional map from node id to file path for resolving paths
+ * @returns Structured text output suitable for LLM consumption
+ */
+export function formatCycles(cycles, nodeToFile) {
+    if (cycles.length === 0) {
+        return 'cycles: none\nstatus: no circular dependencies detected\n';
+    }
+    const resolve = (id) => nodeToFile?.get(id) ?? id;
+    const lines = [
+        `cycles: ${cycles.length} circular dependency group(s) found`,
+        '',
+    ];
+    // Sort by cycle length ascending, then alphabetically
+    const sorted = [...cycles].sort((a, b) => {
+        if (a.length !== b.length)
+            return a.length - b.length;
+        return resolve(a[0]).localeCompare(resolve(b[0]));
+    });
+    sorted.forEach((cycle, i) => {
+        const isSelfLoop = cycle.length === 1;
+        const label = isSelfLoop ? 'self-loop' : `cycle(${cycle.length})`;
+        lines.push(`[${i + 1}] ${label}`);
+        for (const node of cycle) {
+            lines.push(`  file: ${resolve(node)}:1`);
+        }
+        if (!isSelfLoop) {
+            // Show the closing edge
+            lines.push(`  closes: ${resolve(cycle[cycle.length - 1])} → ${resolve(cycle[0])}`);
+        }
+        lines.push('');
+    });
+    const selfLoopCount = sorted.filter(c => c.length === 1).length;
+    const multiNodeCount = sorted.length - selfLoopCount;
+    lines.push(`summary: ${multiNodeCount} multi-node cycle(s), ${selfLoopCount} self-loop(s)`);
+    return lines.join('\n');
+}
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package/dist/src/graph/dead-code.d.ts

@@ -10,4 +10,27 @@ import type { MonographDb } from '../storage/db.js';
  * @returns Array of node ids that are considered dead code.
  */
 export declare function detectDeadCode(db: MonographDb): string[];
+export interface DeadCodeNode {
+    id: string;
+    name: string;
+    filePath: string | null;
+    startLine: number | null;
+    label: string;
+}
+/**
+ * Like detectDeadCode() but returns rich node objects with filePath and
+ * startLine so callers can render file:line navigation hints.
+ *
+ * @param db - The MonographDb instance
+ * @returns Array of dead-code nodes with location metadata.
+ */
+export declare function detectDeadCodeNodes(db: MonographDb): DeadCodeNode[];
+/**
+ * Format dead-code nodes as structured text for LLM consumption.
+ * Each entry includes a file:line navigation hint where available.
+ *
+ * @param nodes - Result from detectDeadCodeNodes()
+ * @returns Multi-line string suitable for injection into LLM context
+ */
+export declare function formatDeadCode(nodes: DeadCodeNode[]): string;
 //# sourceMappingURL=dead-code.d.ts.map

package/dist/src/graph/dead-code.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"dead-code.d.ts","sourceRoot":"","sources":["../../../src/graph/dead-code.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD;;;;;;;;;GASG;AACH,wBAAgB,cAAc,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,CAExD;AAID,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,EAAE,EAAE,WAAW,GAAG,YAAY,EAAE,CAwCnE;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,MAAM,CAqB5D"}

package/dist/src/graph/dead-code.js

@@ -9,26 +9,66 @@
  * @returns Array of node ids that are considered dead code.
  */
 export function detectDeadCode(db) {
-    const nodeRows = db.prepare('SELECT id, is_exported FROM nodes').all();
+    return detectDeadCodeNodes(db).map(n => n.id);
+}
+/**
+ * Like detectDeadCode() but returns rich node objects with filePath and
+ * startLine so callers can render file:line navigation hints.
+ *
+ * @param db - The MonographDb instance
+ * @returns Array of dead-code nodes with location metadata.
+ */
+export function detectDeadCodeNodes(db) {
+    const nodeRows = db
+        .prepare('SELECT id, name, file_path, start_line, label, is_exported FROM nodes')
+        .all();
     if (nodeRows.length === 0)
         return [];
-    // Count in-degrees
+    // Count in-degrees via a single SQL aggregation — avoids loading all edges into JS
+    const inDegreeRows = db
+        .prepare('SELECT target_id, COUNT(*) AS cnt FROM edges WHERE source_id != target_id GROUP BY target_id')
+        .all();
     const inDegree = new Map();
-    for (const { id } of nodeRows) {
-        inDegree.set(id, 0);
-    }
-    const edgeRows = db.prepare('SELECT target_id FROM edges WHERE source_id != target_id').all();
-    for (const { target_id } of edgeRows) {
-        if (inDegree.has(target_id)) {
-            inDegree.set(target_id, (inDegree.get(target_id) ?? 0) + 1);
-        }
+    for (const { target_id, cnt } of inDegreeRows) {
+        inDegree.set(target_id, cnt);
     }
     const dead = [];
-    for (const { id, is_exported } of nodeRows) {
-        if ((inDegree.get(id) ?? 0) === 0 && is_exported !== 1) {
-            dead.push(id);
+    for (const row of nodeRows) {
+        if ((inDegree.get(row.id) ?? 0) === 0 && row.is_exported !== 1) {
+            dead.push({
+                id: row.id,
+                name: row.name,
+                filePath: row.file_path,
+                startLine: row.start_line,
+                label: row.label,
+            });
         }
     }
     return dead;
 }
+/**
+ * Format dead-code nodes as structured text for LLM consumption.
+ * Each entry includes a file:line navigation hint where available.
+ *
+ * @param nodes - Result from detectDeadCodeNodes()
+ * @returns Multi-line string suitable for injection into LLM context
+ */
+export function formatDeadCode(nodes) {
+    if (nodes.length === 0) {
+        return 'Dead code: none detected.';
+    }
+    const lines = [
+        `Dead code: ${nodes.length} unreachable node${nodes.length === 1 ? '' : 's'} detected`,
+        '',
+    ];
+    for (const node of nodes) {
+        const loc = node.filePath != null
+            ? node.startLine != null
+                ? `${node.filePath}:${node.startLine}`
+                : node.filePath
+            : '(unknown location)';
+        lines.push(`  [${node.label}] ${node.name} — ${loc}`);
+    }
+    return lines.join('\n');
+}
 //# sourceMappingURL=dead-code.js.map

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package/dist/src/graph/dependency-closure.d.ts.map

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