fix(coding-agent): load symlinked AGENTS.md in nested git worktrees

The nested worktree dedup compared the context file's realpath with the
main repo's file, so a worktree AGENTS.md symlinked to the main repo's
copy was skipped along with it. Compare the walked directory's realpath
plus the file name instead.

fixes #10681

packages/coding-agent/CHANGELOG.md

@@ -13,6 +13,7 @@
 ### Fixed
 
 - Fixed Mistral streams being aborted mid-generation (e.g. during long thinking) after the request timeout; the timeout now applies only to waiting for response headers ([#10609](https://github.com/earendil-works/pi/issues/10609))
+- Fixed a symlinked `AGENTS.md` in a git worktree nested inside its main repo causing no project context file to load ([#10681](https://github.com/earendil-works/pi/issues/10681))
 
 ## [1.1.0] - 2026-10-07
 

packages/coding-agent/src/core/resource-loader.ts

@@ -252,8 +252,12 @@ export function loadProjectContextFiles(options: {
 
 	while (true) {
 		const contextFile = loadContextFileFromDir(currentDir);
+		// Compare the directory's real path, not the file's: a worktree AGENTS.md that
+		// symlinks to the main repo's file resolves to the shadowed path itself.
 		const isShadowed =
-			shadowedContextFile !== undefined && canonicalizePath(contextFile?.path ?? "") === shadowedContextFile;
+			shadowedContextFile !== undefined &&
+			contextFile !== null &&
+			join(canonicalizePath(currentDir), basename(contextFile.path)) === shadowedContextFile;
 		if (contextFile && !isShadowed && !seenPaths.has(contextFile.path)) {
 			ancestorContextFiles.unshift(contextFile);
 			seenPaths.add(contextFile.path);

packages/coding-agent/test/resource-loader.test.ts

@@ -1243,6 +1243,29 @@ export default function(pi: ExtensionAPI) {
 			expect(files.map((f) => f.content)).toEqual(["worktree instructions"]);
 		});
 
+		// https://github.com/earendil-works/pi/issues/10681
+		it("should load the worktree's context once when it symlinks to the main repo's file", () => {
+			const { main, worktree, worktreeSrc } = setupNestedWorktree();
+			writeFileSync(join(main, "AGENTS.md"), "main repo instructions");
+			symlinkSync(join(main, "AGENTS.md"), join(worktree, "AGENTS.md"));
+
+			const files = loadProjectContextFiles({ cwd: worktreeSrc, agentDir });
+
+			expect(files.map((f) => f.path)).toEqual([join(worktree, "AGENTS.md")]);
+		});
+
+		it("should skip the main repo's duplicate when the main repo's file is a symlink", () => {
+			const { outer, main, worktree, worktreeSrc } = setupNestedWorktree();
+			const shared = join(outer, "shared-agents.md");
+			writeFileSync(shared, "shared instructions");
+			symlinkSync(shared, join(main, "AGENTS.md"));
+			symlinkSync(shared, join(worktree, "AGENTS.md"));
+
+			const files = loadProjectContextFiles({ cwd: worktreeSrc, agentDir });
+
+			expect(files.map((f) => f.path)).toEqual([join(worktree, "AGENTS.md")]);
+		});
+
 		it("should still inherit the main repo's context when the worktree root has none", () => {
 			const { main, worktreeSrc } = setupNestedWorktree();
 			writeFileSync(join(main, "AGENTS.md"), "main repo instructions");