diff --git a/packages/cli/src/__tests__/score.test.ts b/packages/cli/src/__tests__/score.test.ts
index 4691df6..5a5fdc8 100644
--- a/packages/cli/src/__tests__/score.test.ts
+++ b/packages/cli/src/__tests__/score.test.ts
@@ -228,6 +228,60 @@ DEFAULT_LOAD:
     expect(report.signals.agentConfig.manifest.path).toBe('.ai/manifest.adf');
     expect(findCategory(report, 'architecture')?.summary).not.toContain('no ADF manifest');
   });
+
+  it('grounding checker does not count URLs, env-var assignments, Windows paths, or HTTP routes as broken file references', async () => {
+    const tmp = createTempRepo();
+    process.chdir(tmp);
+
+    fs.writeFileSync(path.join(tmp, 'package.json'), JSON.stringify({ name: 'fp-test', version: '1.0.0' }, null, 2));
+
+    // CLAUDE.md intentionally contains every false-positive category from issues #163/#164.
+    // None of these strings should appear in the broken-path list.
+    fs.writeFileSync(path.join(tmp, 'CLAUDE.md'), `# Rules
+
+Env var assignment in a code block: \`AEGIS_LOCAL_URL=http://localhost:11434\`
+Windows absolute path: \`C:/Users/kover/Documents/aegis-daemon\`
+Bare Windows path fragment in prose: Files/Git/mingw64/bin/git-credential-manager.exe
+
+HTTP API routes (from a routes table):
+| /chat | Chat endpoint |
+| /api/runs | Run list |
+| /webhooks/voice/complete | Voice webhook |
+
+URL-only link: [docs](https://example.com/guide)
+
+Hostname with port: localhost:3000
+`);
+
+    const { report } = await captureJson(() => scoreCommand(baseOptions, []));
+
+    const broken: string[] = report.signals.grounding.pathReferences.broken;
+
+    // None of the false-positive patterns should appear as broken references
+    expect(broken.some((b: string) => b.includes('localhost:11434'))).toBe(false);
+    expect(broken.some((b: string) => b.includes('AEGIS_LOCAL_URL'))).toBe(false);
+    expect(broken.some((b: string) => /^[A-Za-z]:[\\/]/.test(b) || b.startsWith('C:/'))).toBe(false);
+    expect(broken.some((b: string) => b === '/chat' || b === '/api/runs' || b.startsWith('/webhooks/'))).toBe(false);
+    expect(broken.some((b: string) => b.includes('example.com'))).toBe(false);
+    expect(broken.some((b: string) => b === 'localhost:3000')).toBe(false);
+  });
+
+  it('grounding checker correctly tracks ./path-without-extension as a broken reference', async () => {
+    const tmp = createTempRepo();
+    process.chdir(tmp);
+
+    fs.writeFileSync(path.join(tmp, 'package.json'), JSON.stringify({ name: 'rel-test', version: '1.0.0' }, null, 2));
+
+    // ./docs/runbooks has no file extension — it must still be tracked because the explicit
+    // ./ prefix makes the intent unambiguous. Regression for the normalizePathCandidate
+    // stripping ./ before the prefix check ran.
+    fs.writeFileSync(path.join(tmp, 'CLAUDE.md'), 'See ./docs/runbooks for on-call procedures.\n');
+
+    const { report } = await captureJson(() => scoreCommand(baseOptions, []));
+
+    const broken: string[] = report.signals.grounding.pathReferences.broken;
+    expect(broken).toContain('docs/runbooks');
+  });
 });
 
 function createTempRepo(): string {
diff --git a/packages/cli/src/commands/score.ts b/packages/cli/src/commands/score.ts
index f94abda..a47115b 100644
--- a/packages/cli/src/commands/score.ts
+++ b/packages/cli/src/commands/score.ts
@@ -980,18 +980,28 @@ function isSubstantiveInstruction(content: string): boolean {
 function extractPathCandidates(content: string): string[] {
   const candidates = new Set<string>();
 
+  // Markdown link targets: [text](path)
   for (const match of content.matchAll(/\[[^\]]+\]\(([^)]+)\)/g)) {
     const target = normalizePathCandidate(match[1]);
     if (looksLikePath(target)) candidates.add(target);
   }
 
+  // Backtick inline code: `path`
   for (const match of content.matchAll(/`([^`\n]+)`/g)) {
     const candidate = normalizePathCandidate(match[1]);
     if (looksLikePath(candidate)) candidates.add(candidate);
   }
 
+  // Raw path patterns in prose/tables — require explicit relative prefix (./  ../) or a known
+  // file extension. This avoids false positives from Windows path fragments, cross-repo refs,
+  // and HTTP route tables captured in freeform text.
+  // NOTE: check `raw` (pre-normalization) for the ./ prefix — normalizePathCandidate strips it,
+  // so checking the already-normalized candidate would silently drop ./path-without-extension refs.
   for (const match of content.matchAll(/(^|[\s(])((?:\.{1,2}\/)?(?:[A-Za-z0-9._-]+\/)*[A-Za-z0-9._-]+(?:\.[A-Za-z0-9._-]+)?)/gm)) {
-    const candidate = normalizePathCandidate(match[2]);
+    const raw = match[2];
+    const candidate = normalizePathCandidate(raw);
+    const ext = path.posix.extname(candidate).toLowerCase();
+    if (!raw.startsWith('./') && !raw.startsWith('../') && !KNOWN_PATH_EXTENSIONS.has(ext)) continue;
     if (looksLikePath(candidate)) candidates.add(candidate);
   }
 
@@ -1009,7 +1019,8 @@ function normalizePathCandidate(raw: string): string {
 }
 
 function resolveReferencedPath(sourceFile: string, candidate: string): ResolvedPathReference {
-  if (candidate.startsWith('/')) {
+  // path.isAbsolute handles both Unix (/foo) and Windows (C:\foo, C:/foo) absolute paths.
+  if (path.isAbsolute(candidate) || candidate.startsWith('/')) {
     return {
       source: sourceFile,
       candidate,
@@ -1030,10 +1041,26 @@ function resolveReferencedPath(sourceFile: string, candidate: string): ResolvedP
 
 function looksLikePath(candidate: string): boolean {
   if (!candidate) return false;
-  if (candidate.startsWith('http://') || candidate.startsWith('https://') || candidate.startsWith('mailto:')) return false;
+  // URL schemes
+  if (candidate.startsWith('http://') || candidate.startsWith('https://') || candidate.startsWith('mailto:') || candidate.startsWith('ftp://')) return false;
+  // CLI flags and fragment anchors
   if (candidate.startsWith('#') || candidate.startsWith('--')) return false;
+  // Template expressions, globs, angle-bracket types
   if (candidate.includes('<') || candidate.includes('>') || candidate.includes('*') || candidate.includes('${')) return false;
+  // Spaces mean prose, not a path
   if (candidate.includes(' ')) return false;
+  // Env-var assignments pulled from code blocks (DATABASE_URL=postgres://...)
+  if (candidate.includes('=')) return false;
+  // Windows drive-letter absolute paths (C:\..., D:/...)
+  if (/^[A-Za-z]:[\\/]/.test(candidate)) return false;
+  // hostname:port patterns (localhost:3000, api.example.com:8080)
+  if (/^[a-zA-Z0-9][a-zA-Z0-9.-]*:[0-9]+$/.test(candidate)) return false;
+  // HTTP API route paths (/api/v1/users) — starts with slash, multiple path segments, no known extension
+  if (
+    candidate.startsWith('/') &&
+    !KNOWN_PATH_EXTENSIONS.has(path.posix.extname(candidate).toLowerCase()) &&
+    candidate.split('/').filter(Boolean).length > 1
+  ) return false;
   if (KNOWN_PATH_FILENAMES.has(candidate) || KNOWN_PATH_FILENAMES.has(path.posix.basename(candidate))) return true;
   if (candidate.includes('/')) return true;
   return KNOWN_PATH_EXTENSIONS.has(path.posix.extname(candidate).toLowerCase());