From b67d9f288f0ef71b02c6ef229bf596fc7e25883a Mon Sep 17 00:00:00 2001
From: garrytan <garrytan@gmail.com>
Date: Mon, 26 Oct 2026 03:00:25 +0000
Subject: [PATCH] fix(context-bill): a root container skips a nested skill
 reached through a directory link at any depth

Co-authored-by: capy-ai[bot] <230910855+capy-ai[bot]@users.noreply.github.com>
---
 lib/context-bill.ts       | 17 ++++++++++++-----
 test/context-bill.test.ts | 26 ++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 5 deletions(-)

diff --git a/lib/context-bill.ts b/lib/context-bill.ts
index 716bf6781..e0552c787 100644
--- a/lib/context-bill.ts
+++ b/lib/context-bill.ts
@@ -284,7 +284,11 @@ export interface WalkedFile {
  *
  * With `skipNestedSkills`, a top-level subdirectory holding its own SKILL.md is
  * not entered, so a container skill keeps the files it shares with a nested
- * skill instead of losing them to whichever path sorted first.
+ * skill instead of losing them to whichever path sorted first. The root
+ * container also skips a nested skill reached through a directory link at any
+ * depth: discovery bills that skill on its own, and the plain walk this
+ * replaced never followed directory links, so counting it here too would bill
+ * it twice.
  *
  * Every directory is read through its realpath, so a lookup crosses at most
  * one link however deep the lexical path runs: a chain of links never hits
@@ -301,8 +305,9 @@ export function walkMdFiles(dir: string, opts: { billedRoot?: string; skipNested
     return out;
   }
   const seen = new Set<string>([rootReal]);
+  const container = rootReal === billedReal;
   let entryCount = 0;
-  const walk = (current: string, currentReal: string) => {
+  const walk = (current: string, currentReal: string, viaLink: boolean) => {
     let entries: fs.Dirent[];
     try {
       entries = fs.readdirSync(currentReal, { withFileTypes: true });
@@ -320,7 +325,9 @@ export function walkMdFiles(dir: string, opts: { billedRoot?: string; skipNested
       } else if (
         kind !== "dir" ||
         fs.existsSync(path.join(viaReal, ".git")) ||
-        (opts.skipNestedSkills && current === dir && isFile(path.join(viaReal, "SKILL.md")))
+        (opts.skipNestedSkills &&
+          (current === dir || (container && (viaLink || e.isSymbolicLink()))) &&
+          isFile(path.join(viaReal, "SKILL.md")))
       ) {
         continue;
       }
@@ -347,10 +354,10 @@ export function walkMdFiles(dir: string, opts: { billedRoot?: string; skipNested
       }
       if (encloses(real, rootReal) || encloses(real, billedReal)) continue;
       seen.add(real);
-      walk(p, real);
+      walk(p, real, viaLink || e.isSymbolicLink());
     }
   };
-  walk(dir, rootReal);
+  walk(dir, rootReal, false);
   return out;
 }
 
diff --git a/test/context-bill.test.ts b/test/context-bill.test.ts
index c82156295..12b9f0ba2 100644
--- a/test/context-bill.test.ts
+++ b/test/context-bill.test.ts
@@ -398,6 +398,32 @@ describe("upstream fix b: installed-tree layout (repo-checkout subdir skip)", ()
     fs.rmSync(root, { recursive: true, force: true });
   });
 
+  it("keeps a root container from billing a nested skill that a deeper directory link reaches", () => {
+    if (process.platform === "win32") return;
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), "context-bill-container-deep-"));
+    fs.writeFileSync(path.join(root, "SKILL.md"), "---\nname: c\ndescription: d\n---\n# c\n");
+    fs.mkdirSync(path.join(root, "sub"));
+    fs.writeFileSync(path.join(root, "sub", "SKILL.md"), "---\nname: s\ndescription: d\n---\n# s\n");
+    fs.writeFileSync(path.join(root, "sub", "big.md"), "b".repeat(10_000));
+    fs.mkdirSync(path.join(root, "refs"));
+    fs.writeFileSync(path.join(root, "refs", "note.md"), "n");
+    fs.symlinkSync(path.join(root, "sub"), path.join(root, "refs", "alias"));
+    const outside = fs.mkdtempSync(path.join(os.tmpdir(), "context-bill-container-outside-"));
+    fs.mkdirSync(path.join(outside, "deep"));
+    fs.writeFileSync(path.join(outside, "deep", "SKILL.md"), "---\nname: o\ndescription: d\n---\n# o\n");
+    fs.writeFileSync(path.join(outside, "deep", "o.md"), "o".repeat(5_000));
+    fs.mkdirSync(path.join(root, "linked"));
+    fs.symlinkSync(outside, path.join(root, "linked", "via"));
+
+    const bill = buildBill(root);
+    const byName = Object.fromEntries(bill.skills.map((s) => [s.name, s]));
+    fs.rmSync(root, { recursive: true, force: true });
+    fs.rmSync(outside, { recursive: true, force: true });
+    expect(Object.keys(byName).sort()).toEqual([path.basename(root), path.join("linked", "via", "deep"), path.join("refs", "alias"), "sub"].sort());
+    expect(byName[path.basename(root)].totalMdBytes).toBe("---\nname: c\ndescription: d\n---\n# c\n".length + 1);
+    expect(byName[path.join("refs", "alias")].totalMdBytes).toBe(byName.sub.totalMdBytes);
+  });
+
   it("walks a chain of links deeper than the kernel's link limit without losing files", () => {
     if (process.platform === "win32") return;
     const tmp = fs.mkdtempSync(path.join(os.tmpdir(), "context-bill-deep-chain-"));