Library → Highlights

Every highlight you make in a PDF, web page, or EPUB collects here — across documents, across formats, searchable and exportable.

Where highlights come from

Select text and highlight it in any preview window that supports markup:

• PDF reader — highlights plus sticky notes
• Web pages (.html / .mhtml)
• EPUB reader

Highlights live in project-managed sidecar files under .scholardo/annotations/ and never modify the original. The mechanics are in Annotations.

Trial and licensing

Creating and editing highlights requires a valid license. Once a license expires, existing highlights still display, read, and export normally — you just can't make new ones or change them.

What a row shows

Each row shows the quoted text, its source document, and any tags. You can:

• Favorite / Unfavorite
• Click through to the position in the original

Orphan highlights

If the source document changes — you re-downloaded a different edition of the PDF, the web page was redesigned — some highlights can no longer anchor back. Those are marked orphan, and the list warns "N orphan annotation(s) — source text has drifted."

They aren't deleted; the content is intact. They've just lost the ability to jump back to the original. The filter can isolate them.

Creating a note

Select some highlights → Create Note from these highlights and they're collected into a new note in Notes.

This is the main channel from reading to writing: mark things up as you read, then pull a batch into one structured note.

Exporting

The export menu covers two formats and two destinations:

	Markdown	CSV
To clipboard	Copy as Markdown	Copy as CSV
To a file	Save as Markdown…	Save as CSV…

Scope is either all (Export all…) or just the selection (Export N selected…).

Hypothesis sync

If you annotate the open web with Hypothesis, you can sync those in. Sync now in the toolbar pulls your Hypothesis annotations and merges them into this list.

One-way sync

This is Hypothesis → Scholardo only. Highlights you make in Scholardo are not pushed back to Hypothesis.

Failures show "sync failed" inline and can be retried.

Agents can read, not write

Agents reach your annotations through three MCP tools:

• list_annotations — every annotation on a document
• get_annotation — one by ID
• search_annotations — by text or tag

All three are read-only. Agents can summarize, compare, and find connections across your markup, but cannot create or modify annotations — what you mark up stays yours.

Going deeper

• Annotations — where highlights are stored, how anchoring works, multi-device caveats