silica-agent 0.24.0

Let an LLM read, write and organize your Markdown notes, and take back any edit it gets wrong.

Point Silica at a folder of notes, PDFs or code. It answers from what is there, brings new material in,
and checks every write it makes: parsed, validated, read back, and reverted if it does not hold.

_{A real 748-note vault, written in Italian, so the answers are too: a question answered from the notes it found,
then the vault as a graph, one note's reading path, the study queue, and the audit. Recorded with Qwen3.5-9B.}

Install

uv tool install "silica-agent[gui,mcp]"

Needs Python 3.11+ and uv. With pipx: pipx install "silica-agent[gui,mcp]".

Quickstart

cd ~/notes        # any folder of .md files, adopted as it is
silica init       # pick a model: a hosted API key, or a local LM Studio / Ollama model
silica --gui      # opens http://localhost:8765; plain `silica` opens the terminal instead

Then type /report. It is read-only: it writes one file, GRAPH_REPORT.md, and shows the hubs, bridges and orphans already in your vault. Search and the graph work with no model at all.

_{The audit as a tab: what holds the vault together, the areas it sorts itself into, and how its links are spread.}

What you can do

Silica is single-user: one person, one vault. There are no per-person permissions and no vault shared between people.

Bring documents in. Slides, case files, papers and mail become notes in the source's own words, not a summary of them.

• /nucleate Inbox/ takes a folder, a glob or one file (PDF, DOCX, EPUB, PPTX, notebooks). Each file is one transaction, checked against what you already have. Stop it whenever; it resumes.
• The vault's + imports files, a whole folder or a link into Inbox/ with no chat turn; a YouTube link gives the video's transcript, and /fetch <url> does the same from the chat. A file dropped on the chat stays that chat's until you press "add to vault".
• A long document is split at its headings into parts of at most 40,000 characters. A PDF page with no text, or with formulas its text layer loses, is read from its image by the model, up to 60 pages a file.
• A note keeps its source's DOI, arXiv id, authors and title, so it can be cited without reopening the document. With Zotero linked, a paper's note opens under its byline, with links to Zotero, the PDF and the DOI.
• /mail import keeps only the threads you took part in, from a mail client's export or Google Takeout, and writes nothing until --apply.
• In a git repository, /wiki writes an ARCHITECTURE.md plus a note per subsystem under docs/silica/, and /stale flags the notes whose code changed shape since.

Ask, with the sources in view. An answer comes from your notes and shows which ones.

• /explain, /compare, /summarize and the chat answer from your notes and cite them. What the vault does not hold is refused, not filled in; /web is the explicit way out, cited from the pages it actually opened.

• Each cited note gets a number. Clicking it opens the note at the line closest to the paragraph that cites it, when enough of their words match; pointing at it lights every paragraph that cites the same note.

• A line under the answer counts the notes read, the steps and the seconds, and lists under "not cited" the notes it read and did not cite.

• A number in the answer that is in no note the chat read and in nothing you typed is listed under it: "numbers not in what this turn read".

• Each note /nucleate writes carries a ## Sources block that leads to the source's verbatim copy in sources/. Search leaves those copies out, so a source never competes with the notes made from it.

• Ask the last question again, or edit it. The chat also searches your earlier chats for what was asked and answered.

  
  _{Every claim links to the note it came from; a link with no note behind it says so.}

Study (Learn). Questions on your notes, graded against the source each note rests on.

• /learn and the Learn tab ask ten kinds of question, from recall and cloze to transfer and contradiction, and correct you by quoting the source line the note rests on. When the note says more than its source, the answer reads "Source mismatch" and is not scored. /quiz re-tests what is fading, scheduled with FSRS-6.

• Before the reveal you say how sure you are: certain (90), pretty sure (70), half unsure (50), guessing (25), or skip. The grader never sees it, nor the session or the chat. Caps come after, in code: a hint or "Just tell me" caps the rating at Hard, and a right answer given while guessing caps at Good.

• After 10 unassisted answers with a confidence, Calibration sets what you said against how often you met the criteria, level by level.

• "Explain it" closes the book: you explain a note in your own words, a student who has not read it asks 4 questions, and your explanation is then checked against the note and its source.

• No single score: estimated retention, depth (Facts, Parts, Mechanisms, New contexts), the relations you answered on and the misconceptions noted are shown apart. A note never asked counts as never practised, not as failed.

• 3 misses in a row on a note put a worked example from it one click away; it never appears unasked. A plan over a folder, some notes or a topic paces you to its date, and that day shows in the Calendar.

  
  _{Questions waiting from earlier sessions, the ones you missed, and your plans.}

See how notes connect. The vault as a map: what sits together, what joins it, and what to read first.

• /path "RAG" "Transformers" walks the reading path between two notes over your wikilinks and the concept graph, /relate names the kind of each link, /graph and /map draw it.

  
  _{One note in its reading order: what to read first, and what it unlocks.}

• On the graph, a click makes a note the centre of its own map. In 2D the areas can be drawn as blobs, one ribbon standing for the links between two of them, and the semantic zones, notes grouped by meaning rather than by links, as outlines over them.

• In Explore, Folders shades each folder by how much it mixes areas. Areas shows one area and the links to its neighbours over the coupling of every pair, each link with the sentence that carries it. Read gives the whole vault a reading order from its hubs.

• Compare one folder, area or zone with another: the panel says what characterises each and quotes the links that join them.

• Click a concept to light the notes that treat it; a second concept narrows them to the notes that treat both, and the panel quotes the lines.

_{The same vault in 3D, coloured by the 23 areas it sorts itself into. A note's size is how much the vault routes through it.}

Trust what it writes. Every write is checked, shown to you and reversible.

• Each write is a card in the chat with its revert. When the check is unsure, the card says why, shows the changed lines and asks you to keep or revert it.
• /undo one note, /revert <run-id> one run, /revert --source paper.pdf everything one document produced, however far it spread. A deleted note waits in the trash until you bring it back or delete it for good.
• When a new source contradicts a note, the contradiction stays written on the note until you resolve it; /contested lists them.
• A flashcard whose answer is not in the note it cites is dropped before you see it; a slide point that is not in its note is named under the deck.
• /verify vouches for a note as you, bound to its text. /stale lists the notes whose source changed and the notes Silica wrote that were since edited by hand.

Organise without moving files. Files stay where you put them; Silica groups and remembers around them.

• A workspace is a note that gathers notes and folders from anywhere in the vault, by list, by folder or by a frontmatter value, plus the notes made from them. A chat opened in it searches only there and reads the workspace's text as standing instructions.
• Vault instructions, written once in Settings, are read by every chat over the vault.
• Silica keeps what a later chat will need and says so in the answer, unless the chat has brought in outside text such as a web page or a file. /memory shows what it holds, /remember saves your words as typed, /incognito keeps a chat off the record.
• The Calendar holds events, deadlines and the day each study plan is due; click or drag an empty time to add an event, with a reminder if you want one. /agenda lists a day or a week.
• A request you make in 3 separate chats, never undone, becomes a proposed skill drafted from your own words. It runs only once you install it from Settings › Skills.
• /curate plans links, orphans and duplicates, and /aliases proposes other names for note titles; both write only with --apply.

How a write is checked

The model never touches a file. It proposes; a parser and a state machine decide.

Benchmarks

Every number comes from a committed result file in evals/, run on the product path.

Small samples, a flash-class judge, 2 of LoCoMo's 10 conversations: not comparable to vendor numbers, but re-runnable on your machine. The unflattering rows ship too: /organize agrees with a human's folders 32% of the time.

Use it from

Coding agents (Claude Code, Codex, any MCP client) use silica-core, the retrieval engine Silica is built on, with no model in the loop.

git clone https://github.com/kiycoh/silica-agent && cd silica-agent
SILICA_VAULT_HOST=~/notes docker compose up -d gui   # http://localhost:8765; your OPENROUTER_API_KEY passes through

License

AGPL-3.0-or-later. A commercial license covers proprietary embedding or a modified hosted service without releasing source. Contributing: CONTRIBUTING.md.