@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/graph/prune.js

@@ -0,0 +1,82 @@
+/**
+ * Remove edges whose source or target node does not exist in the nodes table.
+ *
+ * @param db - The MonographDb instance (better-sqlite3 Database)
+ * @returns The number of dangling edges pruned
+ */
+export function pruneDanglingEdges(db) {
+    // Single-statement DELETE avoids fetching all dangling IDs then re-binding them
+    // as SQL variables (which would fail when edge count exceeds SQLITE_MAX_VARIABLE_NUMBER).
+    const result = db.prepare(`
+    DELETE FROM edges
+    WHERE NOT EXISTS (SELECT 1 FROM nodes n WHERE n.id = source_id)
+       OR NOT EXISTS (SELECT 1 FROM nodes n WHERE n.id = target_id)
+  `).run();
+    return result.changes;
+}
+/**
+ * Remove non-File nodes that have no incoming or outgoing edges.
+ * Leaves File nodes in place so they can still be queried even if isolated.
+ *
+ * @param db - The MonographDb instance
+ * @returns Number of orphan nodes removed
+ */
+export function pruneOrphanNodes(db) {
+    const result = db.prepare(`
+    DELETE FROM nodes
+    WHERE label != 'File'
+      AND NOT EXISTS (SELECT 1 FROM edges WHERE source_id = nodes.id OR target_id = nodes.id)
+  `).run();
+    return result.changes;
+}
+/**
+ * Remove File nodes whose file_path no longer exists on disk.
+ * Also cascades to remove any edges connected to those nodes (via pruneDanglingEdges).
+ *
+ * @param db - The MonographDb instance
+ * @param existingPaths - Set of file paths that currently exist on disk
+ * @returns Number of stale File nodes removed (call pruneDanglingEdges after to clean edges)
+ */
+export function pruneStaleFileNodes(db, existingPaths) {
+    const staleRows = db.prepare(`SELECT id, file_path FROM nodes WHERE label = 'File' AND file_path IS NOT NULL`).all();
+    let removed = 0;
+    const deleteStmt = db.prepare(`DELETE FROM nodes WHERE id = ?`);
+    const tx = db.transaction(() => {
+        for (const row of staleRows) {
+            if (!existingPaths.has(row.file_path)) {
+                deleteStmt.run(row.id);
+                removed++;
+            }
+        }
+    });
+    tx();
+    return removed;
+}
+/**
+ * Run a full prune pass: dangling edges → orphan nodes → stale file nodes.
+ * Optionally pass existingPaths to also remove deleted-file nodes.
+ */
+export function pruneAll(db, existingPaths) {
+    const danglingEdgesRemoved = pruneDanglingEdges(db);
+    const orphanNodesRemoved = pruneOrphanNodes(db);
+    const staleFileNodesRemoved = existingPaths ? pruneStaleFileNodes(db, existingPaths) : 0;
+    // A second dangling-edge pass cleans up any edges left by stale file node removal
+    if (staleFileNodesRemoved > 0)
+        pruneDanglingEdges(db);
+    return { danglingEdgesRemoved, orphanNodesRemoved, staleFileNodesRemoved };
+}
+/**
+ * Format a PruneResult as structured text for LLM consumption.
+ */
+export function formatPruneResult(result) {
+    const total = result.danglingEdgesRemoved + result.orphanNodesRemoved + result.staleFileNodesRemoved;
+    if (total === 0)
+        return 'Prune pass: nothing to remove — graph is clean.';
+    return [
+        `Prune pass removed ${total} artifact(s):`,
+        `  dangling edges:    ${result.danglingEdgesRemoved}`,
+        `  orphan nodes:      ${result.orphanNodesRemoved}`,
+        `  stale file nodes:  ${result.staleFileNodesRemoved}`,
+    ].join('\n');
+}
+//# sourceMappingURL=prune.js.map

package/dist/src/graph/prune.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/re-exports/propagate.d.ts

@@ -0,0 +1,11 @@
+import type { ModuleNode } from '../node-types.js';
+export interface Edge {
+    sourceIdx: number;
+    targetIdx: number;
+    importedName?: string;
+    exportedName?: string;
+    isTypeOnly: boolean;
+}
+export declare function propagateStarReExport(modules: ModuleNode[], edges: Edge[], edgesByTarget: Map<number, number[]>, barrelId: number, barrelIdx: number, sourceIdx: number, entryStarTargets: Set<number>): boolean;
+export declare function propagateNamedReExport(modules: ModuleNode[], barrelId: number, barrelIdx: number, sourceIdx: number, importedName: string, exportedName: string, existingRefs: Set<number>): boolean;
+//# sourceMappingURL=propagate.d.ts.map

package/dist/src/graph/re-exports/propagate.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/graph/re-exports/propagate.js

@@ -0,0 +1,51 @@
+export function propagateStarReExport(modules, edges, edgesByTarget, barrelId, barrelIdx, sourceIdx, entryStarTargets) {
+    const barrel = modules[barrelIdx];
+    const source = modules[sourceIdx];
+    const before = barrel.exports.length;
+    const existingNames = new Set(barrel.exports.map(e => e.name));
+    for (const sym of source.exports) {
+        if (!existingNames.has(sym.name)) {
+            barrel.exports.push({ ...sym, isReExport: true });
+            existingNames.add(sym.name);
+        }
+    }
+    const changed = barrel.exports.length > before;
+    if (changed && entryStarTargets.has(barrelId)) {
+        const upstreamEdgeIndices = edgesByTarget.get(barrelIdx) ?? [];
+        for (const ei of upstreamEdgeIndices) {
+            const edge = edges[ei];
+            if (edge.importedName === undefined) {
+                propagateStarReExport(modules, edges, edgesByTarget, modules[edge.targetIdx].fileId, edge.targetIdx, barrelIdx, entryStarTargets);
+            }
+        }
+    }
+    return changed;
+}
+export function propagateNamedReExport(modules, barrelId, barrelIdx, sourceIdx, importedName, exportedName, existingRefs) {
+    const source = modules[sourceIdx];
+    const barrel = modules[barrelIdx];
+    const sourceSym = source.exports.find(e => e.name === importedName);
+    if (!sourceSym)
+        return false;
+    const existing = barrel.exports.find(e => e.name === exportedName);
+    if (existing)
+        return false;
+    barrel.exports.push({
+        name: exportedName,
+        isType: sourceSym.isType,
+        isReExport: true,
+        line: sourceSym.line,
+    });
+    for (const refId of existingRefs) {
+        const refIdx = modules.findIndex(m => m.fileId === refId);
+        if (refIdx !== -1) {
+            const refMod = modules[refIdx];
+            const alreadyRefs = refMod.references.some(r => r.name === exportedName && r.fromFile === barrel.filePath);
+            if (!alreadyRefs) {
+                refMod.references.push({ name: exportedName, kind: 'Unknown', fromFile: barrel.filePath });
+            }
+        }
+    }
+    return true;
+}
+//# sourceMappingURL=propagate.js.map

package/dist/src/graph/re-exports/propagate.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/reachability.d.ts

@@ -0,0 +1,9 @@
+import { ModuleNode } from './node-types.js';
+export interface ReachabilityOptions {
+    runtimeEntries?: Set<number>;
+    testEntries?: Set<number>;
+}
+export declare function markReachable(nodes: Map<number, ModuleNode>, edges: Map<number, number[]>, entryPoints: number[], opts?: ReachabilityOptions): void;
+export declare function collectReachable(nodes: Map<number, ModuleNode>): Set<number>;
+export declare function collectUnreachable(nodes: Map<number, ModuleNode>, allFileIds: number[]): number[];
+//# sourceMappingURL=reachability.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/src/graph/reachability.js

@@ -0,0 +1,72 @@
+import { ModuleNodeFlags, setFlag } from './node-types.js';
+function bfsReachable(nodes, edges, entryPoints) {
+    const visited = new Set();
+    const queue = [];
+    for (const ep of entryPoints) {
+        if (nodes.has(ep) && !visited.has(ep)) {
+            visited.add(ep);
+            queue.push(ep);
+        }
+    }
+    let i = 0;
+    while (i < queue.length) {
+        const current = queue[i++];
+        const neighbors = edges.get(current) ?? [];
+        for (const neighbor of neighbors) {
+            if (!visited.has(neighbor) && nodes.has(neighbor)) {
+                visited.add(neighbor);
+                queue.push(neighbor);
+            }
+        }
+    }
+    return visited;
+}
+function setsEqual(a, b) {
+    if (a.size !== b.size)
+        return false;
+    for (const v of a) {
+        if (!b.has(v))
+            return false;
+    }
+    return true;
+}
+export function markReachable(nodes, edges, entryPoints, opts) {
+    const entrySet = new Set(entryPoints);
+    const visited = bfsReachable(nodes, edges, entryPoints);
+    const runtimeEntries = opts?.runtimeEntries;
+    const testEntries = opts?.testEntries;
+    const runtimeSame = runtimeEntries === undefined || setsEqual(runtimeEntries, entrySet);
+    const runtimeVisited = runtimeSame
+        ? null
+        : bfsReachable(nodes, edges, [...(runtimeEntries ?? [])]);
+    const testVisited = !testEntries || testEntries.size === 0
+        ? null
+        : bfsReachable(nodes, edges, [...testEntries]);
+    for (const [id, node] of nodes) {
+        if (visited.has(id)) {
+            setFlag(node, ModuleNodeFlags.REACHABLE);
+        }
+        if (runtimeVisited ? runtimeVisited.has(id) : visited.has(id)) {
+            setFlag(node, ModuleNodeFlags.RUNTIME_REACHABLE);
+        }
+        if (testVisited?.has(id)) {
+            setFlag(node, ModuleNodeFlags.TEST_REACHABLE);
+        }
+    }
+}
+export function collectReachable(nodes) {
+    const result = new Set();
+    for (const [id, node] of nodes) {
+        if ((node.flags & ModuleNodeFlags.REACHABLE) !== 0) {
+            result.add(id);
+        }
+    }
+    return result;
+}
+export function collectUnreachable(nodes, allFileIds) {
+    return allFileIds.filter(id => {
+        const node = nodes.get(id);
+        return !node || (node.flags & ModuleNodeFlags.REACHABLE) === 0;
+    });
+}
+//# sourceMappingURL=reachability.js.map

package/dist/src/graph/reachability.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/regex-search.d.ts

@@ -0,0 +1,41 @@
+import type { MonographNode, MonographEdge } from '../types.js';
+import type { MonographDb } from '../storage/db.js';
+export interface RegexNodeMatch {
+    node: MonographNode;
+    /** Which field of the node matched. */
+    field: 'name' | 'filePath' | 'language' | 'label';
+}
+/**
+ * Search nodes whose name, filePath, language, or label matches the given
+ * regular expression.
+ *
+ * @param db      - The MonographDb instance.
+ * @param pattern - A RegExp (or a string that will be compiled to one).
+ * @param fields  - Which fields to test; default: ['name', 'filePath'].
+ */
+export declare function regexSearchNodes(db: MonographDb, pattern: RegExp | string, fields?: Array<'name' | 'filePath' | 'language' | 'label'>, limit?: number): RegexNodeMatch[];
+export interface RegexEdgeMatch {
+    edge: MonographEdge;
+    /** Which field of the edge matched. */
+    field: 'relation' | 'confidence' | 'reason';
+}
+/**
+ * Search edges whose relation, confidence, or reason matches the given
+ * regular expression.
+ *
+ * @param db      - The MonographDb instance.
+ * @param pattern - A RegExp (or a string that will be compiled to one).
+ * @param fields  - Which fields to test; default: ['relation', 'reason'].
+ */
+export declare function regexSearchEdges(db: MonographDb, pattern: RegExp | string, fields?: Array<'relation' | 'confidence' | 'reason'>, limit?: number): RegexEdgeMatch[];
+export declare function regexSearchNodesInMemory(nodes: MonographNode[], pattern: RegExp | string, fields?: Array<'name' | 'filePath' | 'language' | 'label'>): RegexNodeMatch[];
+export declare function regexSearchEdgesInMemory(edges: MonographEdge[], pattern: RegExp | string, fields?: Array<'relation' | 'confidence' | 'reason'>): RegexEdgeMatch[];
+/**
+ * Format node regex match results as structured text for LLM consumption.
+ */
+export declare function formatRegexNodeMatches(matches: RegexNodeMatch[], pattern: string): string;
+/**
+ * Format edge regex match results as structured text for LLM consumption.
+ */
+export declare function formatRegexEdgeMatches(matches: RegexEdgeMatch[], pattern: string): string;
+//# sourceMappingURL=regex-search.d.ts.map

package/dist/src/graph/regex-search.d.ts.map

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package/dist/src/graph/regex-search.js

@@ -0,0 +1,140 @@
+/**
+ * Search nodes whose name, filePath, language, or label matches the given
+ * regular expression.
+ *
+ * @param db      - The MonographDb instance.
+ * @param pattern - A RegExp (or a string that will be compiled to one).
+ * @param fields  - Which fields to test; default: ['name', 'filePath'].
+ */
+export function regexSearchNodes(db, pattern, fields = ['name', 'filePath'], limit = 200) {
+    const re = typeof pattern === 'string' ? new RegExp(pattern) : pattern;
+    const rows = db.prepare(`SELECT id, label, name, norm_label, file_path, start_line, end_line,
+            community_id, is_exported, language, properties
+     FROM nodes LIMIT ?`).all(limit);
+    const results = [];
+    for (const r of rows) {
+        const node = {
+            id: r.id,
+            label: r.label,
+            name: r.name,
+            normLabel: r.norm_label,
+            filePath: r.file_path ?? undefined,
+            startLine: r.start_line ?? undefined,
+            endLine: r.end_line ?? undefined,
+            communityId: r.community_id ?? undefined,
+            isExported: r.is_exported === 1,
+            language: r.language ?? undefined,
+            properties: r.properties ? JSON.parse(r.properties) : undefined,
+        };
+        for (const field of fields) {
+            const value = field === 'name' ? r.name :
+                field === 'filePath' ? (r.file_path ?? '') :
+                    field === 'language' ? (r.language ?? '') :
+                        r.label;
+            if (value && re.test(value)) {
+                results.push({ node, field });
+                break; // report once per node even if multiple fields match
+            }
+        }
+    }
+    return results;
+}
+/**
+ * Search edges whose relation, confidence, or reason matches the given
+ * regular expression.
+ *
+ * @param db      - The MonographDb instance.
+ * @param pattern - A RegExp (or a string that will be compiled to one).
+ * @param fields  - Which fields to test; default: ['relation', 'reason'].
+ */
+export function regexSearchEdges(db, pattern, fields = ['relation', 'reason'], limit = 200) {
+    const re = typeof pattern === 'string' ? new RegExp(pattern) : pattern;
+    const rows = db.prepare(`SELECT id, source_id, target_id, relation, confidence, confidence_score, reason
+     FROM edges LIMIT ?`).all(limit);
+    const results = [];
+    for (const r of rows) {
+        const edge = {
+            id: r.id,
+            sourceId: r.source_id,
+            targetId: r.target_id,
+            relation: r.relation,
+            confidence: r.confidence,
+            confidenceScore: r.confidence_score,
+            reason: r.reason ?? undefined,
+        };
+        for (const field of fields) {
+            const value = field === 'relation' ? r.relation :
+                field === 'confidence' ? r.confidence :
+                    (r.reason ?? '');
+            if (value && re.test(value)) {
+                results.push({ edge, field });
+                break;
+            }
+        }
+    }
+    return results;
+}
+// ── In-memory variants ─────────────────────────────────────────────────────────
+export function regexSearchNodesInMemory(nodes, pattern, fields = ['name', 'filePath']) {
+    const re = typeof pattern === 'string' ? new RegExp(pattern) : pattern;
+    const results = [];
+    for (const node of nodes) {
+        for (const field of fields) {
+            const value = field === 'name' ? node.name :
+                field === 'filePath' ? (node.filePath ?? '') :
+                    field === 'language' ? (node.language ?? '') :
+                        node.label;
+            if (value && re.test(value)) {
+                results.push({ node, field });
+                break;
+            }
+        }
+    }
+    return results;
+}
+export function regexSearchEdgesInMemory(edges, pattern, fields = ['relation', 'reason']) {
+    const re = typeof pattern === 'string' ? new RegExp(pattern) : pattern;
+    const results = [];
+    for (const edge of edges) {
+        for (const field of fields) {
+            const value = field === 'relation' ? edge.relation :
+                field === 'confidence' ? edge.confidence :
+                    (edge.reason ?? '');
+            if (value && re.test(value)) {
+                results.push({ edge, field });
+                break;
+            }
+        }
+    }
+    return results;
+}
+// ── LLM formatters ─────────────────────────────────────────────────────────────
+/**
+ * Format node regex match results as structured text for LLM consumption.
+ */
+export function formatRegexNodeMatches(matches, pattern) {
+    if (matches.length === 0)
+        return `No nodes matching /${pattern}/.`;
+    const lines = [`${matches.length} node(s) matching /${pattern}/:`];
+    for (const m of matches) {
+        const loc = m.node.filePath
+            ? ` ${m.node.filePath}${m.node.startLine != null ? `:${m.node.startLine}` : ''}`
+            : '';
+        lines.push(`  [${m.field}] ${m.node.label} ${m.node.name}${loc}`);
+    }
+    return lines.join('\n');
+}
+/**
+ * Format edge regex match results as structured text for LLM consumption.
+ */
+export function formatRegexEdgeMatches(matches, pattern) {
+    if (matches.length === 0)
+        return `No edges matching /${pattern}/.`;
+    const lines = [`${matches.length} edge(s) matching /${pattern}/:`];
+    for (const m of matches) {
+        lines.push(`  [${m.field}] ${m.edge.sourceId} -[${m.edge.relation}]-> ${m.edge.targetId}` +
+            (m.edge.reason ? `  // ${m.edge.reason}` : ''));
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=regex-search.js.map

package/dist/src/graph/regex-search.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/regression.d.ts

@@ -0,0 +1,48 @@
+import type Database from 'better-sqlite3';
+export declare class Tolerance {
+    private readonly pct;
+    private readonly value;
+    private constructor();
+    /**
+     * Parse a tolerance specification.
+     * Accepts "2%" (percentage relative to baseline) or "5" (absolute count).
+     * Throws if the spec is malformed or negative.
+     */
+    static parse(spec: string): Tolerance;
+    /**
+     * Returns true if the delta from baseline to current exceeds tolerance.
+     * Only positive deltas (regressions) can violate tolerance.
+     * Special case: if baseline is 0 and current > 0, percentage tolerance is always exceeded.
+     */
+    exceeded(baseline: number, current: number): boolean;
+    toString(): string;
+}
+export interface RegressionMetric {
+    metric: string;
+    baseline: number;
+    current: number;
+    delta: number;
+    tolerance: string;
+    violated: boolean;
+}
+export interface RegressionOutcome {
+    passed: boolean;
+    violations: RegressionMetric[];
+    checkedMetrics: RegressionMetric[];
+    summary: string;
+}
+/**
+ * Compare current DB state against a named baseline.
+ *
+ * @param db - better-sqlite3 Database instance
+ * @param baselinePath - path to the baseline JSON file
+ * @param toleranceSpec - e.g. "5%" or "10" — applied to ALL metrics unless metricTolerances provided
+ * @param metricTolerances - per-metric tolerance overrides, e.g. { godNodeCount: "2", surpriseCount: "10%" }
+ */
+export declare function checkRegression(db: Database.Database, baselinePath: string, toleranceSpec: string, metricTolerances?: Record<string, string>): RegressionOutcome;
+/**
+ * Format a RegressionOutcome as structured text for LLM consumption.
+ * Shows pass/fail status, per-metric results, and actionable violation details.
+ */
+export declare function formatRegressionOutcome(outcome: RegressionOutcome): string;
+//# sourceMappingURL=regression.d.ts.map

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

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