@weavelogic/knowledge-graph-agent 0.6.0 → 0.7.1

package/dist/cli/commands/hive-mind/analyze-links.js

@@ -0,0 +1,367 @@
+import { Command } from "commander";
+import chalk from "chalk";
+import * as path from "path";
+import { writeFile, access, readFile } from "fs/promises";
+import { glob } from "fast-glob";
+import matter from "gray-matter";
+class LinkAnalyzer {
+  fileMap = /* @__PURE__ */ new Map();
+  allFiles = /* @__PURE__ */ new Set();
+  /**
+   * Analyze a vault for links and build adjacency list
+   */
+  async analyzeVault(vaultPath, options = {}) {
+    const resolvedPath = path.resolve(vaultPath);
+    try {
+      await access(resolvedPath);
+    } catch {
+      throw new Error(`Vault path does not exist: ${resolvedPath}`);
+    }
+    const files = await glob("**/*.md", {
+      cwd: resolvedPath,
+      ignore: ["node_modules/**", ".git/**", "dist/**"],
+      absolute: false
+    });
+    if (files.length === 0) {
+      throw new Error(`No markdown files found in: ${resolvedPath}`);
+    }
+    this.buildFileMap(files);
+    const adjacencyList = /* @__PURE__ */ new Map();
+    const brokenLinks = [];
+    const incomingLinks = /* @__PURE__ */ new Map();
+    let totalWikiLinks = 0;
+    let totalMarkdownLinks = 0;
+    let maxLinksInFile = 0;
+    let maxLinksFile = "";
+    for (const file of files) {
+      adjacencyList.set(file, []);
+      incomingLinks.set(file, /* @__PURE__ */ new Set());
+    }
+    for (const file of files) {
+      const filePath = path.join(resolvedPath, file);
+      const content = await readFile(filePath, "utf-8");
+      const { content: bodyContent } = matter(content);
+      const wikiLinks = this.parseWikiLinks(bodyContent);
+      const markdownLinks = this.parseMarkdownLinks(bodyContent);
+      totalWikiLinks += wikiLinks.length;
+      totalMarkdownLinks += markdownLinks.length;
+      const fileLinks = adjacencyList.get(file) || [];
+      const totalLinksInThisFile = wikiLinks.length + markdownLinks.length;
+      if (totalLinksInThisFile > maxLinksInFile) {
+        maxLinksInFile = totalLinksInThisFile;
+        maxLinksFile = file;
+      }
+      for (const link of wikiLinks) {
+        const resolved = this.resolveLink(link, file);
+        if (resolved && this.allFiles.has(resolved)) {
+          fileLinks.push(resolved);
+          incomingLinks.get(resolved)?.add(file);
+        } else {
+          brokenLinks.push({
+            source: file,
+            target: link,
+            type: "wikilink"
+          });
+        }
+      }
+      for (const link of markdownLinks) {
+        const resolved = this.resolveLink(link, file);
+        if (resolved && this.allFiles.has(resolved)) {
+          fileLinks.push(resolved);
+          incomingLinks.get(resolved)?.add(file);
+        } else if (!this.isExternalLink(link)) {
+          brokenLinks.push({
+            source: file,
+            target: link,
+            type: "markdown"
+          });
+        }
+      }
+      adjacencyList.set(file, [...new Set(fileLinks)]);
+    }
+    const orphanFiles = [];
+    for (const file of files) {
+      const outgoing = adjacencyList.get(file) || [];
+      const incoming = incomingLinks.get(file) || /* @__PURE__ */ new Set();
+      if (outgoing.length === 0 && incoming.size === 0) {
+        orphanFiles.push(file);
+      }
+    }
+    const totalFiles = files.length;
+    const filesWithLinks = files.filter((f) => {
+      const outgoing = adjacencyList.get(f) || [];
+      const incoming = incomingLinks.get(f) || /* @__PURE__ */ new Set();
+      return outgoing.length > 0 || incoming.size > 0;
+    }).length;
+    const orphanRate = totalFiles > 0 ? orphanFiles.length / totalFiles * 100 : 0;
+    const totalLinks = totalWikiLinks + totalMarkdownLinks;
+    const linkDensity = totalFiles > 0 ? totalLinks / totalFiles : 0;
+    const averageLinksPerFile = totalFiles > 0 ? totalLinks / totalFiles : 0;
+    const isolatedClusters = this.countClusters(adjacencyList, files);
+    return {
+      totalFiles,
+      filesWithLinks,
+      orphanFiles,
+      orphanRate: Math.round(orphanRate * 100) / 100,
+      linkDensity: Math.round(linkDensity * 100) / 100,
+      adjacencyList,
+      brokenLinks,
+      statistics: {
+        totalLinks,
+        wikiLinks: totalWikiLinks,
+        markdownLinks: totalMarkdownLinks,
+        averageLinksPerFile: Math.round(averageLinksPerFile * 100) / 100,
+        maxLinksInFile,
+        maxLinksFile,
+        isolatedClusters
+      }
+    };
+  }
+  /**
+   * Build a map from filename (without extension) to full path
+   */
+  buildFileMap(files) {
+    this.fileMap.clear();
+    this.allFiles.clear();
+    for (const file of files) {
+      this.allFiles.add(file);
+      const basename = path.basename(file, ".md");
+      if (!this.fileMap.has(basename)) {
+        this.fileMap.set(basename, file);
+      }
+      const pathWithoutExt = file.replace(/\.md$/, "");
+      this.fileMap.set(pathWithoutExt, file);
+    }
+  }
+  /**
+   * Parse [[wiki-links]] from content
+   * Handles: [[link]], [[link|alias]], [[folder/link]], [[link#heading]]
+   */
+  parseWikiLinks(content) {
+    const links = [];
+    const regex = /\[\[([^\]|#]+)(?:#[^\]|]*)?(?:\|[^\]]+)?\]\]/g;
+    let match;
+    while ((match = regex.exec(content)) !== null) {
+      const link = match[1].trim();
+      if (link) {
+        links.push(link);
+      }
+    }
+    return links;
+  }
+  /**
+   * Parse [markdown](links) from content
+   * Handles: [text](link.md), [text](./link.md), [text](../folder/link.md)
+   */
+  parseMarkdownLinks(content) {
+    const links = [];
+    const regex = /(?<!!)\[([^\]]*)\]\(([^)]+)\)/g;
+    let match;
+    while ((match = regex.exec(content)) !== null) {
+      const link = match[2].trim();
+      if (link && !this.isExternalLink(link) && !link.startsWith("#")) {
+        links.push(link);
+      }
+    }
+    return links;
+  }
+  /**
+   * Check if a link is external (http, https, etc.)
+   */
+  isExternalLink(link) {
+    return /^(https?:|mailto:|tel:|ftp:)/i.test(link);
+  }
+  /**
+   * Resolve a link to a file in the vault
+   */
+  resolveLink(link, sourceFile) {
+    let cleanLink = link.replace(/\.md$/, "");
+    if (cleanLink.startsWith("./") || cleanLink.startsWith("../")) {
+      const sourceDir = path.dirname(sourceFile);
+      const resolved = path.normalize(path.join(sourceDir, cleanLink));
+      cleanLink = resolved;
+    }
+    const found = this.fileMap.get(cleanLink);
+    if (found) return found;
+    const withMd = cleanLink + ".md";
+    if (this.allFiles.has(withMd)) return withMd;
+    const basename = path.basename(cleanLink);
+    const byBasename = this.fileMap.get(basename);
+    if (byBasename) return byBasename;
+    return null;
+  }
+  /**
+   * Count isolated clusters using union-find algorithm
+   */
+  countClusters(adjacencyList, files) {
+    const parent = /* @__PURE__ */ new Map();
+    const rank = /* @__PURE__ */ new Map();
+    for (const file of files) {
+      parent.set(file, file);
+      rank.set(file, 0);
+    }
+    const find = (x) => {
+      if (parent.get(x) !== x) {
+        parent.set(x, find(parent.get(x)));
+      }
+      return parent.get(x);
+    };
+    const union = (x, y) => {
+      const rootX = find(x);
+      const rootY = find(y);
+      if (rootX !== rootY) {
+        const rankX = rank.get(rootX) || 0;
+        const rankY = rank.get(rootY) || 0;
+        if (rankX < rankY) {
+          parent.set(rootX, rootY);
+        } else if (rankX > rankY) {
+          parent.set(rootY, rootX);
+        } else {
+          parent.set(rootY, rootX);
+          rank.set(rootX, rankX + 1);
+        }
+      }
+    };
+    for (const [source, targets] of adjacencyList) {
+      for (const target of targets) {
+        if (parent.has(target)) {
+          union(source, target);
+        }
+      }
+    }
+    const roots = /* @__PURE__ */ new Set();
+    for (const file of files) {
+      roots.add(find(file));
+    }
+    return roots.size;
+  }
+  /**
+   * Generate a detailed report
+   */
+  generateReport(result) {
+    const lines = [];
+    lines.push("# Link Analysis Report\n");
+    lines.push(`Generated: ${(/* @__PURE__ */ new Date()).toISOString()}
+`);
+    lines.push("## Summary\n");
+    lines.push(`| Metric | Value |`);
+    lines.push(`|--------|-------|`);
+    lines.push(`| Total Files | ${result.totalFiles} |`);
+    lines.push(`| Files with Links | ${result.filesWithLinks} |`);
+    lines.push(`| Orphan Files | ${result.orphanFiles.length} |`);
+    lines.push(`| Orphan Rate | ${result.orphanRate}% |`);
+    lines.push(`| Link Density | ${result.linkDensity} |`);
+    lines.push(`| Total Links | ${result.statistics.totalLinks} |`);
+    lines.push(`| Wiki Links | ${result.statistics.wikiLinks} |`);
+    lines.push(`| Markdown Links | ${result.statistics.markdownLinks} |`);
+    lines.push(`| Avg Links/File | ${result.statistics.averageLinksPerFile} |`);
+    lines.push(`| Max Links in File | ${result.statistics.maxLinksInFile} |`);
+    lines.push(`| Most Linked File | ${result.statistics.maxLinksFile} |`);
+    lines.push(`| Isolated Clusters | ${result.statistics.isolatedClusters} |`);
+    lines.push("");
+    if (result.orphanFiles.length > 0) {
+      lines.push("## Orphan Files\n");
+      lines.push("Files with no incoming or outgoing links:\n");
+      for (const file of result.orphanFiles.slice(0, 50)) {
+        lines.push(`- \`${file}\``);
+      }
+      if (result.orphanFiles.length > 50) {
+        lines.push(`
+... and ${result.orphanFiles.length - 50} more`);
+      }
+      lines.push("");
+    }
+    if (result.brokenLinks.length > 0) {
+      lines.push("## Broken Links\n");
+      lines.push("Links that point to non-existent files:\n");
+      for (const broken of result.brokenLinks.slice(0, 50)) {
+        lines.push(`- \`${broken.source}\` -> \`${broken.target}\` (${broken.type})`);
+      }
+      if (result.brokenLinks.length > 50) {
+        lines.push(`
+... and ${result.brokenLinks.length - 50} more`);
+      }
+      lines.push("");
+    }
+    return lines.join("\n");
+  }
+}
+function createAnalyzeLinksCommand() {
+  const command = new Command("analyze-links").description("Analyze wiki-links and markdown links in a vault").argument("<vault-path>", "Path to Obsidian vault or docs directory").option("-o, --output <file>", "Output file for results (JSON or Markdown)").option("--json", "Output as JSON").option("-v, --verbose", "Show detailed output").action(async (vaultPath, options) => {
+    const analyzer = new LinkAnalyzer();
+    console.log(chalk.cyan("\nAnalyzing links in vault...\n"));
+    try {
+      const result = await analyzer.analyzeVault(vaultPath, options);
+      if (options.json) {
+        const jsonResult = {
+          ...result,
+          adjacencyList: Object.fromEntries(result.adjacencyList)
+        };
+        if (options.output) {
+          await writeFile(options.output, JSON.stringify(jsonResult, null, 2));
+          console.log(chalk.green(`Results written to: ${options.output}`));
+        } else {
+          console.log(JSON.stringify(jsonResult, null, 2));
+        }
+      } else {
+        console.log(chalk.bold("Summary:"));
+        console.log(chalk.white(`  Total Files:      ${result.totalFiles}`));
+        console.log(chalk.white(`  Files with Links: ${result.filesWithLinks}`));
+        console.log(chalk.white(`  Orphan Files:     ${chalk.yellow(result.orphanFiles.length.toString())}`));
+        console.log(chalk.white(`  Orphan Rate:      ${chalk.yellow(result.orphanRate + "%")}`));
+        console.log(chalk.white(`  Link Density:     ${result.linkDensity}`));
+        console.log("");
+        console.log(chalk.bold("Link Statistics:"));
+        console.log(chalk.white(`  Total Links:      ${result.statistics.totalLinks}`));
+        console.log(chalk.white(`  Wiki Links:       ${result.statistics.wikiLinks}`));
+        console.log(chalk.white(`  Markdown Links:   ${result.statistics.markdownLinks}`));
+        console.log(chalk.white(`  Avg Links/File:   ${result.statistics.averageLinksPerFile}`));
+        console.log(chalk.white(`  Isolated Clusters: ${result.statistics.isolatedClusters}`));
+        console.log("");
+        if (result.brokenLinks.length > 0) {
+          console.log(chalk.bold(chalk.red(`Broken Links: ${result.brokenLinks.length}`)));
+          if (options.verbose) {
+            for (const broken of result.brokenLinks.slice(0, 10)) {
+              console.log(chalk.red(`  ${broken.source} -> ${broken.target}`));
+            }
+            if (result.brokenLinks.length > 10) {
+              console.log(chalk.gray(`  ... and ${result.brokenLinks.length - 10} more`));
+            }
+          }
+          console.log("");
+        }
+        if (options.verbose && result.orphanFiles.length > 0) {
+          console.log(chalk.bold(chalk.yellow("Orphan Files:")));
+          for (const file of result.orphanFiles.slice(0, 10)) {
+            console.log(chalk.yellow(`  ${file}`));
+          }
+          if (result.orphanFiles.length > 10) {
+            console.log(chalk.gray(`  ... and ${result.orphanFiles.length - 10} more`));
+          }
+          console.log("");
+        }
+        if (options.output) {
+          const report = analyzer.generateReport(result);
+          await writeFile(options.output, report);
+          console.log(chalk.green(`Report written to: ${options.output}`));
+        }
+        console.log(chalk.bold("Target Metrics:"));
+        const orphanStatus = result.orphanRate < 10 ? chalk.green("PASS") : chalk.red("FAIL");
+        const densityStatus = result.linkDensity > 5 ? chalk.green("PASS") : chalk.red("FAIL");
+        console.log(chalk.white(`  Orphan Rate:   ${result.orphanRate}% (target: < 10%) ${orphanStatus}`));
+        console.log(chalk.white(`  Link Density:  ${result.linkDensity} (target: > 5.0) ${densityStatus}`));
+        console.log("");
+      }
+    } catch (error) {
+      console.error(chalk.red("Error:"), error instanceof Error ? error.message : "Unknown error");
+      process.exit(1);
+    }
+  });
+  return command;
+}
+export {
+  LinkAnalyzer,
+  createAnalyzeLinksCommand,
+  createAnalyzeLinksCommand as default
+};
+//# sourceMappingURL=analyze-links.js.map

package/dist/cli/commands/hive-mind/analyze-links.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"analyze-links.js","sources":["../../../../src/cli/commands/hive-mind/analyze-links.ts"],"sourcesContent":["/**\n * Hive Mind - Link Analyzer\n *\n * Analyzes wiki-links and markdown links in a vault to build an adjacency list\n * and identify orphan files.\n *\n * SPEC-003: Hive Mind Reconnection Tools\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport * as path from 'path';\nimport { readFile, access, writeFile } from 'fs/promises';\nimport { glob } from 'fast-glob';\nimport matter from 'gray-matter';\n\n// ============================================================================\n// Types\n// ============================================================================\n\nexport interface AnalyzeOptions {\n  output?: string;\n  json?: boolean;\n  verbose?: boolean;\n  includeContent?: boolean;\n}\n\nexport interface BrokenLink {\n  source: string;\n  target: string;\n  type: 'wikilink' | 'markdown';\n  lineNumber?: number;\n}\n\nexport interface LinkAnalysisResult {\n  totalFiles: number;\n  filesWithLinks: number;\n  orphanFiles: string[];\n  orphanRate: number;\n  linkDensity: number;\n  adjacencyList: Map<string, string[]>;\n  brokenLinks: BrokenLink[];\n  statistics: {\n    totalLinks: number;\n    wikiLinks: number;\n    markdownLinks: number;\n    averageLinksPerFile: number;\n    maxLinksInFile: number;\n    maxLinksFile: string;\n    isolatedClusters: number;\n  };\n}\n\n// ============================================================================\n// Link Analyzer Class\n// ============================================================================\n\nexport class LinkAnalyzer {\n  private fileMap: Map<string, string> = new Map();\n  private allFiles: Set<string> = new Set();\n\n  /**\n   * Analyze a vault for links and build adjacency list\n   */\n  async analyzeVault(vaultPath: string, options: AnalyzeOptions = {}): Promise<LinkAnalysisResult> {\n    const resolvedPath = path.resolve(vaultPath);\n\n    // Check if path exists\n    try {\n      await access(resolvedPath);\n    } catch {\n      throw new Error(`Vault path does not exist: ${resolvedPath}`);\n    }\n\n    // Find all markdown files\n    const files = await glob('**/*.md', {\n      cwd: resolvedPath,\n      ignore: ['node_modules/**', '.git/**', 'dist/**'],\n      absolute: false,\n    });\n\n    if (files.length === 0) {\n      throw new Error(`No markdown files found in: ${resolvedPath}`);\n    }\n\n    // Build file map for resolution (filename without extension -> full path)\n    this.buildFileMap(files);\n\n    const adjacencyList = new Map<string, string[]>();\n    const brokenLinks: BrokenLink[] = [];\n    const incomingLinks = new Map<string, Set<string>>();\n    let totalWikiLinks = 0;\n    let totalMarkdownLinks = 0;\n    let maxLinksInFile = 0;\n    let maxLinksFile = '';\n\n    // Initialize adjacency list and incoming links\n    for (const file of files) {\n      adjacencyList.set(file, []);\n      incomingLinks.set(file, new Set());\n    }\n\n    // Process each file\n    for (const file of files) {\n      const filePath = path.join(resolvedPath, file);\n      const content = await readFile(filePath, 'utf-8');\n\n      // Parse frontmatter to skip it for link counting\n      const { content: bodyContent } = matter(content);\n\n      // Extract links\n      const wikiLinks = this.parseWikiLinks(bodyContent);\n      const markdownLinks = this.parseMarkdownLinks(bodyContent);\n\n      totalWikiLinks += wikiLinks.length;\n      totalMarkdownLinks += markdownLinks.length;\n\n      const fileLinks = adjacencyList.get(file) || [];\n      const totalLinksInThisFile = wikiLinks.length + markdownLinks.length;\n\n      if (totalLinksInThisFile > maxLinksInFile) {\n        maxLinksInFile = totalLinksInThisFile;\n        maxLinksFile = file;\n      }\n\n      // Process wiki links\n      for (const link of wikiLinks) {\n        const resolved = this.resolveLink(link, file);\n        if (resolved && this.allFiles.has(resolved)) {\n          fileLinks.push(resolved);\n          incomingLinks.get(resolved)?.add(file);\n        } else {\n          brokenLinks.push({\n            source: file,\n            target: link,\n            type: 'wikilink',\n          });\n        }\n      }\n\n      // Process markdown links\n      for (const link of markdownLinks) {\n        const resolved = this.resolveLink(link, file);\n        if (resolved && this.allFiles.has(resolved)) {\n          fileLinks.push(resolved);\n          incomingLinks.get(resolved)?.add(file);\n        } else if (!this.isExternalLink(link)) {\n          brokenLinks.push({\n            source: file,\n            target: link,\n            type: 'markdown',\n          });\n        }\n      }\n\n      adjacencyList.set(file, [...new Set(fileLinks)]); // Dedupe\n    }\n\n    // Find orphan files (no incoming AND no outgoing links)\n    const orphanFiles: string[] = [];\n    for (const file of files) {\n      const outgoing = adjacencyList.get(file) || [];\n      const incoming = incomingLinks.get(file) || new Set();\n      if (outgoing.length === 0 && incoming.size === 0) {\n        orphanFiles.push(file);\n      }\n    }\n\n    // Calculate metrics\n    const totalFiles = files.length;\n    const filesWithLinks = files.filter(f => {\n      const outgoing = adjacencyList.get(f) || [];\n      const incoming = incomingLinks.get(f) || new Set();\n      return outgoing.length > 0 || incoming.size > 0;\n    }).length;\n\n    const orphanRate = totalFiles > 0 ? (orphanFiles.length / totalFiles) * 100 : 0;\n    const totalLinks = totalWikiLinks + totalMarkdownLinks;\n    const linkDensity = totalFiles > 0 ? totalLinks / totalFiles : 0;\n    const averageLinksPerFile = totalFiles > 0 ? totalLinks / totalFiles : 0;\n\n    // Calculate isolated clusters using union-find\n    const isolatedClusters = this.countClusters(adjacencyList, files);\n\n    return {\n      totalFiles,\n      filesWithLinks,\n      orphanFiles,\n      orphanRate: Math.round(orphanRate * 100) / 100,\n      linkDensity: Math.round(linkDensity * 100) / 100,\n      adjacencyList,\n      brokenLinks,\n      statistics: {\n        totalLinks,\n        wikiLinks: totalWikiLinks,\n        markdownLinks: totalMarkdownLinks,\n        averageLinksPerFile: Math.round(averageLinksPerFile * 100) / 100,\n        maxLinksInFile,\n        maxLinksFile,\n        isolatedClusters,\n      },\n    };\n  }\n\n  /**\n   * Build a map from filename (without extension) to full path\n   */\n  private buildFileMap(files: string[]): void {\n    this.fileMap.clear();\n    this.allFiles.clear();\n\n    for (const file of files) {\n      this.allFiles.add(file);\n\n      // Map by filename without extension\n      const basename = path.basename(file, '.md');\n      if (!this.fileMap.has(basename)) {\n        this.fileMap.set(basename, file);\n      }\n\n      // Also map by full path without extension\n      const pathWithoutExt = file.replace(/\\.md$/, '');\n      this.fileMap.set(pathWithoutExt, file);\n    }\n  }\n\n  /**\n   * Parse [[wiki-links]] from content\n   * Handles: [[link]], [[link|alias]], [[folder/link]], [[link#heading]]\n   */\n  parseWikiLinks(content: string): string[] {\n    const links: string[] = [];\n    // Match [[link]] and [[link|alias]] patterns\n    const regex = /\\[\\[([^\\]|#]+)(?:#[^\\]|]*)?(?:\\|[^\\]]+)?\\]\\]/g;\n    let match;\n\n    while ((match = regex.exec(content)) !== null) {\n      const link = match[1].trim();\n      if (link) {\n        links.push(link);\n      }\n    }\n\n    return links;\n  }\n\n  /**\n   * Parse [markdown](links) from content\n   * Handles: [text](link.md), [text](./link.md), [text](../folder/link.md)\n   */\n  parseMarkdownLinks(content: string): string[] {\n    const links: string[] = [];\n    // Match [text](link) patterns, excluding images ![...](...) and external links\n    const regex = /(?<!!)\\[([^\\]]*)\\]\\(([^)]+)\\)/g;\n    let match;\n\n    while ((match = regex.exec(content)) !== null) {\n      const link = match[2].trim();\n      // Skip external links, anchors, and non-md files\n      if (link && !this.isExternalLink(link) && !link.startsWith('#')) {\n        links.push(link);\n      }\n    }\n\n    return links;\n  }\n\n  /**\n   * Check if a link is external (http, https, etc.)\n   */\n  private isExternalLink(link: string): boolean {\n    return /^(https?:|mailto:|tel:|ftp:)/i.test(link);\n  }\n\n  /**\n   * Resolve a link to a file in the vault\n   */\n  private resolveLink(link: string, sourceFile: string): string | null {\n    // Remove .md extension if present\n    let cleanLink = link.replace(/\\.md$/, '');\n\n    // Remove leading ./ or ../ and resolve relative paths\n    if (cleanLink.startsWith('./') || cleanLink.startsWith('../')) {\n      const sourceDir = path.dirname(sourceFile);\n      const resolved = path.normalize(path.join(sourceDir, cleanLink));\n      cleanLink = resolved;\n    }\n\n    // Try to find in file map\n    const found = this.fileMap.get(cleanLink);\n    if (found) return found;\n\n    // Try with .md extension\n    const withMd = cleanLink + '.md';\n    if (this.allFiles.has(withMd)) return withMd;\n\n    // Try just the basename (for simple wiki-links)\n    const basename = path.basename(cleanLink);\n    const byBasename = this.fileMap.get(basename);\n    if (byBasename) return byBasename;\n\n    return null;\n  }\n\n  /**\n   * Count isolated clusters using union-find algorithm\n   */\n  private countClusters(adjacencyList: Map<string, string[]>, files: string[]): number {\n    const parent = new Map<string, string>();\n    const rank = new Map<string, number>();\n\n    // Initialize each file as its own cluster\n    for (const file of files) {\n      parent.set(file, file);\n      rank.set(file, 0);\n    }\n\n    const find = (x: string): string => {\n      if (parent.get(x) !== x) {\n        parent.set(x, find(parent.get(x)!));\n      }\n      return parent.get(x)!;\n    };\n\n    const union = (x: string, y: string): void => {\n      const rootX = find(x);\n      const rootY = find(y);\n      if (rootX !== rootY) {\n        const rankX = rank.get(rootX) || 0;\n        const rankY = rank.get(rootY) || 0;\n        if (rankX < rankY) {\n          parent.set(rootX, rootY);\n        } else if (rankX > rankY) {\n          parent.set(rootY, rootX);\n        } else {\n          parent.set(rootY, rootX);\n          rank.set(rootX, rankX + 1);\n        }\n      }\n    };\n\n    // Union connected files\n    for (const [source, targets] of adjacencyList) {\n      for (const target of targets) {\n        if (parent.has(target)) {\n          union(source, target);\n        }\n      }\n    }\n\n    // Count unique roots\n    const roots = new Set<string>();\n    for (const file of files) {\n      roots.add(find(file));\n    }\n\n    return roots.size;\n  }\n\n  /**\n   * Generate a detailed report\n   */\n  generateReport(result: LinkAnalysisResult): string {\n    const lines: string[] = [];\n\n    lines.push('# Link Analysis Report\\n');\n    lines.push(`Generated: ${new Date().toISOString()}\\n`);\n\n    lines.push('## Summary\\n');\n    lines.push(`| Metric | Value |`);\n    lines.push(`|--------|-------|`);\n    lines.push(`| Total Files | ${result.totalFiles} |`);\n    lines.push(`| Files with Links | ${result.filesWithLinks} |`);\n    lines.push(`| Orphan Files | ${result.orphanFiles.length} |`);\n    lines.push(`| Orphan Rate | ${result.orphanRate}% |`);\n    lines.push(`| Link Density | ${result.linkDensity} |`);\n    lines.push(`| Total Links | ${result.statistics.totalLinks} |`);\n    lines.push(`| Wiki Links | ${result.statistics.wikiLinks} |`);\n    lines.push(`| Markdown Links | ${result.statistics.markdownLinks} |`);\n    lines.push(`| Avg Links/File | ${result.statistics.averageLinksPerFile} |`);\n    lines.push(`| Max Links in File | ${result.statistics.maxLinksInFile} |`);\n    lines.push(`| Most Linked File | ${result.statistics.maxLinksFile} |`);\n    lines.push(`| Isolated Clusters | ${result.statistics.isolatedClusters} |`);\n    lines.push('');\n\n    if (result.orphanFiles.length > 0) {\n      lines.push('## Orphan Files\\n');\n      lines.push('Files with no incoming or outgoing links:\\n');\n      for (const file of result.orphanFiles.slice(0, 50)) {\n        lines.push(`- \\`${file}\\``);\n      }\n      if (result.orphanFiles.length > 50) {\n        lines.push(`\\n... and ${result.orphanFiles.length - 50} more`);\n      }\n      lines.push('');\n    }\n\n    if (result.brokenLinks.length > 0) {\n      lines.push('## Broken Links\\n');\n      lines.push('Links that point to non-existent files:\\n');\n      for (const broken of result.brokenLinks.slice(0, 50)) {\n        lines.push(`- \\`${broken.source}\\` -> \\`${broken.target}\\` (${broken.type})`);\n      }\n      if (result.brokenLinks.length > 50) {\n        lines.push(`\\n... and ${result.brokenLinks.length - 50} more`);\n      }\n      lines.push('');\n    }\n\n    return lines.join('\\n');\n  }\n}\n\n// ============================================================================\n// CLI Command\n// ============================================================================\n\nexport function createAnalyzeLinksCommand(): Command {\n  const command = new Command('analyze-links')\n    .description('Analyze wiki-links and markdown links in a vault')\n    .argument('<vault-path>', 'Path to Obsidian vault or docs directory')\n    .option('-o, --output <file>', 'Output file for results (JSON or Markdown)')\n    .option('--json', 'Output as JSON')\n    .option('-v, --verbose', 'Show detailed output')\n    .action(async (vaultPath: string, options: AnalyzeOptions) => {\n      const analyzer = new LinkAnalyzer();\n\n      console.log(chalk.cyan('\\nAnalyzing links in vault...\\n'));\n\n      try {\n        const result = await analyzer.analyzeVault(vaultPath, options);\n\n        if (options.json) {\n          // Convert Map to Object for JSON serialization\n          const jsonResult = {\n            ...result,\n            adjacencyList: Object.fromEntries(result.adjacencyList),\n          };\n\n          if (options.output) {\n            await writeFile(options.output, JSON.stringify(jsonResult, null, 2));\n            console.log(chalk.green(`Results written to: ${options.output}`));\n          } else {\n            console.log(JSON.stringify(jsonResult, null, 2));\n          }\n        } else {\n          // Display summary\n          console.log(chalk.bold('Summary:'));\n          console.log(chalk.white(`  Total Files:      ${result.totalFiles}`));\n          console.log(chalk.white(`  Files with Links: ${result.filesWithLinks}`));\n          console.log(chalk.white(`  Orphan Files:     ${chalk.yellow(result.orphanFiles.length.toString())}`));\n          console.log(chalk.white(`  Orphan Rate:      ${chalk.yellow(result.orphanRate + '%')}`));\n          console.log(chalk.white(`  Link Density:     ${result.linkDensity}`));\n          console.log('');\n\n          console.log(chalk.bold('Link Statistics:'));\n          console.log(chalk.white(`  Total Links:      ${result.statistics.totalLinks}`));\n          console.log(chalk.white(`  Wiki Links:       ${result.statistics.wikiLinks}`));\n          console.log(chalk.white(`  Markdown Links:   ${result.statistics.markdownLinks}`));\n          console.log(chalk.white(`  Avg Links/File:   ${result.statistics.averageLinksPerFile}`));\n          console.log(chalk.white(`  Isolated Clusters: ${result.statistics.isolatedClusters}`));\n          console.log('');\n\n          if (result.brokenLinks.length > 0) {\n            console.log(chalk.bold(chalk.red(`Broken Links: ${result.brokenLinks.length}`)));\n            if (options.verbose) {\n              for (const broken of result.brokenLinks.slice(0, 10)) {\n                console.log(chalk.red(`  ${broken.source} -> ${broken.target}`));\n              }\n              if (result.brokenLinks.length > 10) {\n                console.log(chalk.gray(`  ... and ${result.brokenLinks.length - 10} more`));\n              }\n            }\n            console.log('');\n          }\n\n          if (options.verbose && result.orphanFiles.length > 0) {\n            console.log(chalk.bold(chalk.yellow('Orphan Files:')));\n            for (const file of result.orphanFiles.slice(0, 10)) {\n              console.log(chalk.yellow(`  ${file}`));\n            }\n            if (result.orphanFiles.length > 10) {\n              console.log(chalk.gray(`  ... and ${result.orphanFiles.length - 10} more`));\n            }\n            console.log('');\n          }\n\n          // Write report if output specified\n          if (options.output) {\n            const report = analyzer.generateReport(result);\n            await writeFile(options.output, report);\n            console.log(chalk.green(`Report written to: ${options.output}`));\n          }\n\n          // Show target metrics comparison\n          console.log(chalk.bold('Target Metrics:'));\n          const orphanStatus = result.orphanRate < 10 ? chalk.green('PASS') : chalk.red('FAIL');\n          const densityStatus = result.linkDensity > 5.0 ? chalk.green('PASS') : chalk.red('FAIL');\n          console.log(chalk.white(`  Orphan Rate:   ${result.orphanRate}% (target: < 10%) ${orphanStatus}`));\n          console.log(chalk.white(`  Link Density:  ${result.linkDensity} (target: > 5.0) ${densityStatus}`));\n  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package/dist/cli/commands/hive-mind/find-connections.d.ts

@@ -0,0 +1,75 @@
+/**
+ * Hive Mind - Connection Finder
+ *
+ * Uses TF-IDF similarity to find potential connections between documents.
+ * Suggests links for orphan files to reconnect the knowledge graph.
+ *
+ * SPEC-003: Hive Mind Reconnection Tools
+ */
+import { Command } from 'commander';
+export interface FindConnectionsOptions {
+    threshold?: string;
+    suggest?: boolean;
+    limit?: string;
+    output?: string;
+    json?: boolean;
+    verbose?: boolean;
+}
+export interface SimilarityMatch {
+    source: string;
+    target: string;
+    similarity: number;
+    sharedTerms: string[];
+}
+export interface DocumentVector {
+    file: string;
+    terms: Map<string, number>;
+    magnitude: number;
+}
+export interface ConnectionFinderResult {
+    totalDocuments: number;
+    suggestedConnections: SimilarityMatch[];
+    orphanConnections: SimilarityMatch[];
+    termCount: number;
+    averageSimilarity: number;
+}
+export declare class ConnectionFinder {
+    private documents;
+    private documentVectors;
+    private documentFrequency;
+    private totalDocuments;
+    /**
+     * Build TF-IDF index from vault
+     */
+    buildIndex(vaultPath: string): Promise<void>;
+    /**
+     * Find similar documents to a source file
+     */
+    findSimilar(sourceFile: string, threshold?: number, limit?: number): SimilarityMatch[];
+    /**
+     * Calculate cosine similarity between two document vectors
+     */
+    private cosineSimilarity;
+    /**
+     * Find shared terms between two documents
+     */
+    private findSharedTerms;
+    /**
+     * Suggest connections for orphan files
+     */
+    suggestConnections(vaultPath: string, orphanFiles: string[], threshold?: number, limit?: number): Promise<SimilarityMatch[]>;
+    /**
+     * Find all potential connections above threshold
+     */
+    findAllConnections(vaultPath: string, threshold?: number, limit?: number): Promise<ConnectionFinderResult>;
+    /**
+     * Get index statistics
+     */
+    getStats(): {
+        documents: number;
+        terms: number;
+    };
+}
+export declare function createFindConnectionsCommand(): Command;
+export default createFindConnectionsCommand;
+//# sourceMappingURL=find-connections.d.ts.map

package/dist/cli/commands/hive-mind/find-connections.d.ts.map

@@ -0,0 +1 @@
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