From 178109c22cdcff71455475c445bc79cc8fbb114a Mon Sep 17 00:00:00 2001
From: sharziki <sharvil.saxena@gmail.com>
Date: Sat, 18 Apr 2026 16:01:13 -0400
Subject: [PATCH] fix(extract): skip _-prefixed directories in
 walkMarkdownFiles (#202)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The extract walker matched file-level behavior — `_foo.md` was skipped —
but its recursion still walked into `_pending/originals/`, so
`gbrain extract all --source fs` counted quarantined pages that the
sync path correctly excluded.

On a brain with 61 authoritative pages and a sizeable `_pending/` tree,
extract reported "154 pages walked" instead of 61, wasting link/timeline
extraction effort and producing misleading counts.

Hoist the `_`-prefix skip above the `lstatSync` branch so it applies to
directories as well. Dotted entries already behave this way. Added a
regression test covering a nested `_pending/originals/buried.md` layout
alongside a sibling `concepts/alpha.md` that must still be walked.

Fixes #202
---
 src/commands/extract.ts | 10 +++++++++-
 test/extract.test.ts    | 26 ++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/commands/extract.ts b/src/commands/extract.ts
index 1b5abb7e..9c3c70c7 100644
--- a/src/commands/extract.ts
+++ b/src/commands/extract.ts
@@ -52,12 +52,20 @@ export function walkMarkdownFiles(dir: string): { path: string; relPath: string
   const files: { path: string; relPath: string }[] = [];
   function walk(d: string) {
     for (const entry of readdirSync(d)) {
+      // Skip `.`-prefixed entries (hidden / dotfiles) and `_`-prefixed entries
+      // (user-quarantine convention — e.g. `_pending/` ambient captures) at
+      // BOTH file and directory level. Previously the file-level check
+      // skipped `_foo.md` but the directory recursion still walked into
+      // `_pending/originals/foo.md`, so extract counted quarantined content
+      // that `sync` correctly excluded — "N pages walked" ballooned from 61
+      // to 154 on brains with large `_pending/` trees (issue #202).
       if (entry.startsWith('.')) continue;
+      if (entry.startsWith('_')) continue;
       const full = join(d, entry);
       try {
         if (lstatSync(full).isDirectory()) {
           walk(full);
-        } else if (entry.endsWith('.md') && !entry.startsWith('_')) {
+        } else if (entry.endsWith('.md')) {
           files.push({ path: full, relPath: relative(dir, full) });
         }
       } catch { /* skip unreadable */ }
diff --git a/test/extract.test.ts b/test/extract.test.ts
index 78720eff..698f49a2 100644
--- a/test/extract.test.ts
+++ b/test/extract.test.ts
@@ -122,4 +122,30 @@ describe('walkMarkdownFiles', () => {
   it('is a function', () => {
     expect(typeof walkMarkdownFiles).toBe('function');
   });
+
+  it('skips _-prefixed directories, matching the _-prefixed file behavior', async () => {
+    // Quarantine convention (e.g. `_pending/` for signal-detector ambient
+    // captures): users extend exclusions to skip these paths on sync. The
+    // walker already skipped `_foo.md` files but still recursed into
+    // `_pending/originals/`, so extract counted quarantined content that
+    // sync excluded (issue #202).
+    const { mkdtempSync, writeFileSync, mkdirSync, rmSync } = await import('fs');
+    const { tmpdir } = await import('os');
+    const { join } = await import('path');
+
+    const root = mkdtempSync(join(tmpdir(), 'gbrain-walk-test-'));
+    try {
+      mkdirSync(join(root, 'concepts'));
+      mkdirSync(join(root, '_pending', 'originals'), { recursive: true });
+      writeFileSync(join(root, 'concepts', 'alpha.md'), '# alpha');
+      writeFileSync(join(root, '_pending', 'ambient.md'), '# ambient');
+      writeFileSync(join(root, '_pending', 'originals', 'buried.md'), '# buried');
+      writeFileSync(join(root, '_skip-me.md'), '# file-level skip');
+
+      const files = walkMarkdownFiles(root).map(f => f.relPath).sort();
+      expect(files).toEqual(['concepts/alpha.md']);
+    } finally {
+      rmSync(root, { recursive: true, force: true });
+    }
+  });
 });