fix: enable linked doc navigation in annotate mode

[dgrissen2]

Summary

• Bug: Clicking .md links in annotated files (e.g., [37% IQM](comparison_iqm_37.md)) showed "Failed to connect to server" because the annotate server had no /api/doc endpoint — requests fell through to the SPA catch-all, returning HTML instead of JSON.
• Root cause: The /api/doc handler (handleDoc) was only registered in the plan server (packages/server/index.ts), not the annotate server (packages/server/annotate.ts).
• Fix: Three targeted changes:
  1. annotate.ts — Add /api/doc route, auto-injecting the source file's parent directory as ?base= so relative sibling links (e.g., comparison_iqm_37.md from plots/gamma_segments/comparison_iqm_35.md) resolve from the correct location
  2. reference-handlers.ts — handleDoc() now accepts an optional ?base= query param and tries resolving relative to 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 also resolve correctly

Test plan

• plannotator annotate a markdown file that contains relative .md links to sibling files
• Click a .md link — linked doc should load in-place with back button
• From the linked doc, click another .md link — should resolve relative to that doc's directory
• Click back — should return to the original annotated file
• Plan server linked doc navigation still works (no regression)

🤖 Generated with Claude Code

[backnotprop]

Code review

Found 1 issue:

1. imageBaseDir is referenced but never defined in App.tsx. It is not declared as state, a prop, an import, or a constant anywhere in the file. This will cause a ReferenceError at runtime when a user clicks a relative .md link in annotate mode and linkedDocHook.filepath is null (i.e., the first navigation from the root annotated file). The fallback imageBaseDir is always undefined, so if (baseDir) is false, and the code falls through to linkedDocHook.open(docPath) without any ?base= param — defeating the relative path resolution for the initial hop. It appears the intent was to capture filePath from the /api/plan response (which annotate.ts already sends at line 121) into component state, but that wiring is missing.

plannotator/packages/editor/App.tsx

Lines 508 to 521 in 0477ae3

	} else {
	// 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, imageBaseDir]);

🤖 Generated with Claude Code

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