fix: enable linked doc navigation in annotate mode (#276)

The annotate server was missing the /api/doc endpoint, so clicking
.md links (e.g., [see other](sibling.md)) in annotated files showed
"Failed to connect to server" — the request fell through to the SPA
catch-all and returned HTML instead of JSON.

Three changes:

1. annotate.ts — Add /api/doc route, auto-injecting the source
   file's parent directory as ?base= so relative links resolve
   from the correct location.

2. reference-handlers.ts — handleDoc() now accepts an optional
   ?base= query param and tries resolving relative paths against
   it before falling back to the project-root glob search.

3. App.tsx — handleOpenLinkedDoc passes the current file's
   directory as ?base= when navigating linked-doc → linked-doc,
   so chained relative links resolve correctly.

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: dgrissen2

packages/editor/App.tsx

@@ -529,9 +529,19 @@ const App: React.FC = () => {
     if (vaultBrowser.activeFile && vaultPath) {
       linkedDocHook.open(docPath, buildVaultDocUrl(vaultPath));
     } else {
-      linkedDocHook.open(docPath);
+      // Pass the current file's directory as base for relative path resolution
+      const baseDir = linkedDocHook.filepath
+        ? linkedDocHook.filepath.replace(/\/[^/]+$/, '')
+        : imageBaseDir;
+      if (baseDir) {
+        linkedDocHook.open(docPath, (path) =>
+          `/api/doc?path=${encodeURIComponent(path)}&base=${encodeURIComponent(baseDir)}`
+        );
+      } else {
+        linkedDocHook.open(docPath);
+      }
     }
-  }, [vaultBrowser.activeFile, vaultPath, linkedDocHook, buildVaultDocUrl]);
+  }, [vaultBrowser.activeFile, vaultPath, linkedDocHook, buildVaultDocUrl, imageBaseDir]);
 
   // Wrap linked doc back to also clear vault active file
   const handleLinkedDocBack = React.useCallback(() => {

packages/server/annotate.ts

@@ -14,7 +14,9 @@
 import { isRemoteSession, getServerPort } from "./remote";
 import { getRepoInfo } from "./repo";
 import { handleImage, handleUpload, handleServerReady, handleDraftSave, handleDraftLoad, handleDraftDelete } from "./shared-handlers";
+import { handleDoc } from "./reference-handlers";
 import { contentHash, deleteDraft } from "./draft";
+import { dirname } from "path";
 
 // Re-export utilities
 export { isRemoteSession, getServerPort } from "./remote";
@@ -130,6 +132,17 @@ export async function startAnnotateServer(
             return handleImage(req);
           }
 
+          // API: Serve a linked markdown document
+          // Inject source file's directory as base for relative path resolution
+          if (url.pathname === "/api/doc" && req.method === "GET") {
+            if (!url.searchParams.has("base")) {
+              const docUrl = new URL(req.url);
+              docUrl.searchParams.set("base", dirname(filePath));
+              return handleDoc(new Request(docUrl.toString()));
+            }
+            return handleDoc(req);
+          }
+
           // API: Upload image -> save to temp -> return path
           if (url.pathname === "/api/upload" && req.method === "POST") {
             return handleUpload(req);

packages/server/reference-handlers.ts

@@ -73,6 +73,20 @@ export async function handleDoc(req: Request): Promise<Response> {
     return Response.json({ error: "Missing path parameter" }, { status: 400 });
   }
 
+  // If a base directory is provided, try resolving relative to it first
+  // (used by annotate mode to resolve paths relative to the source file)
+  const base = url.searchParams.get("base");
+  if (base && !requestedPath.startsWith("/") && /\.mdx?$/i.test(requestedPath)) {
+    const fromBase = resolve(base, requestedPath);
+    try {
+      const file = Bun.file(fromBase);
+      if (await file.exists()) {
+        const markdown = await file.text();
+        return Response.json({ markdown, filepath: fromBase });
+      }
+    } catch { /* fall through to standard resolution */ }
+  }
+
   const projectRoot = process.cwd();
   const result = await resolveMarkdownFile(requestedPath, projectRoot);