Silica Core

Silica indexes the markdown, code, PDFs and office files under one root and serves them to Claude Code, Cursor, Hermes, Codex, OpenCode and every other popular harness, as MCP tools or as shell commands that print the same JSON. A hit is a path, a section, a line, a window of text and the numbers to judge it by. The harness owns the loop.

[the quickstart recorded end to end: uv tool install, silica-core init reporting nine indexed documents, silica-core setup claude registering the MCP server, then Claude Code answering a question about the LSM compaction design space by calling silica-core and citing the PDF with its page and its line]

Three commands, then a question asked the way you would ask any other. The harness calls silica_search, and the answer carries the file, the page and the line it came from.

Install

In Claude Code, install the plugin instead: it brings its own server, dense leg included.

uv tool install 'silica-core[mcp]'         # BM25 over documents and their sections (faster, lighter)uv tool install 'silica-core[mcp,dense]'   # in addition the dense leg: numpy, a static model (still fast, more precise)

The second line adds the dense leg: numpy and a static model2vec model, no torch and no GPU. It stays inert until the model is named and the sections are embedded — the last stanza of the Quickstart. Take it when the questions are paraphrases that share no words with the text; an exact term or an identifier is answered by the lexical leg either way, and only that leg reports terms_absent.

pipx works the same. The package and the command are silica-core, the tools are silica_*.

Upgrading from 0.9 or older: the silica command is silica-core since 0.10.0 (silica belongs to silica-harness). A client registered by an older silica setup still launches silica mcp, which stops starting once uvx fetches 0.10.0. Run silica-core setup <client> once and it rewrites that entry.

Quickstart

In any folder of markdown, code, PDFs or office files:

silica-core init                              # adopt the folder: ignore file, vault.yaml, first index; the MCP server serves adopted folders onlysilica-core search "leveled compaction" -k 5  # the best located passagessilica-core setup claude                      # register the MCP server, write the guidance block into ~/.claude/CLAUDE.md
# optional, with the [dense] extra: the dense leg, a static model, nothing leaves the machineexport SILICA_EMBEDDING_MODEL=model2vec/minishlab/potion-retrieval-32Msilica-core index --embed

[silica-core search "leveled compaction" over nine LSM papers: the hit carries the file, p. 5 and the passage; beside it the PDF is open on that page with the same passage highlighted]

Nine arXiv papers, indexed in 2.1 s. The hit names the file, the page and the passage; the page beside it is the check.

Tools

In a source tree every function, method, class and constant is its own unit: a hit's section is the symbol, span its lines, and silica_read(path, section=…) serves the body. For a symbol whose name is known, grep wins; for a question that names none, the search comes first: the tool description and the block silica-core setup claude writes say so. The contract, the reply shapes and the acceptance checks are in TOOLS.md. Nothing needs an API key or a network.

How search says no

A ranked list always has a top, even when the corpus does not answer. Three fields say how much the result is worth:

• coverage: the share of the query's idf mass the hit's matched terms carry. Near 1, every rare term matched; near 0, only common words did.
• terms_absent: query terms that occur nowhere in the corpus.
• matched_terms: the words this hit actually contains.

[silica-core search "raft consensus log replication" over the same nine papers: terms_absent lists raft and consensus, coverage falls to 0.19, and the top hit is a passage about data replication rather than Raft]

raft consensus log replication over the same nine papers: raft and consensus occur in none of them, coverage falls to 0.19, and the top hit is about data replication. On 254 papers the top hit of an answered question carries 0.69 to 1.00; a question the corpus does not cover, 0.44. Silica exposes the signals; the harness decides whether to stop, read or rephrase.

What a reply also says (0.12)

Asked in November 2026, nine models named what they need from a knowledge layer; each of these was kept only where a probe on a production model showed the failure it fixes (TOOLS.md has the numbers):

• scope counts every file the search could not read, an office file with no extracted .md beside it included, so a folder of .docx no longer reads as silent.
• A hit from a converted note carries source_state: stale when its PDF was replaced after the conversion, before the passage is quoted.
• terms_near offers the corpus's closest spelling of an absent word (quitanllu → quitanlu) instead of leaving a misspelt name to read as absent.
• unseen counts the ranked documents as strong as the weakest shown that were not shown; exclude takes the paths already read and serves the next ones, so a long list is paged instead of re-fetched.
• silica_files(since=…) lists only what changed after a time, dated: what changed since the last session.

Benchmarks

nDCG@10 on BEIR SciFact · NFCorpus, the same documents and queries for every arm. BEIR's published BM25 baselines are 0.665 · 0.325. Silica's lexical index needs no model; the others serve lexical search from an index that also holds embeddings.

Code, on the twenty SWE-QA questions zvec-grep publishes for its own benchmark, same embedder, k = 10, scored on the files and symbols the reference answer rests on.

On BEIR the two hybrids tie at the 95% interval: the same vectors rank the same, with no daemon and no vector store. On code, Silica's hybrid file MRR is +0.135 over zvec-grep's hybrid (95% interval +0.01 to +0.27), paired per question. The fusion also gains +0.21 MRR and +0.30 symbol hit over Silica's lexical arm; no reranker or graph expansion is involved.

On this measured scope, Silica is a compact, local, SOTA-competitive retriever: it matches zvec-grep on BEIR and leads the paired SWE-QA code-localization replay with the same embedder.

Retrieval matters only if the agent does less work without losing the answer. These are separate experiments and are not pooled:

The repository result is one repetition: turns improve by 1.75 (95% interval 0.55 to 3.05 fewer), while Judge and cost remain inconclusive. The document rows belong to a 144-run study over twelve questions and a 5.5M-token corpus. They establish less work on that workload, not a universal agent claim.

Corpora, intervals, per-task exceptions and reproduction commands are in benchmarks.

Harnesses

silica-core setup <client> writes the registration into the client's own config and backs up what was there; for claude it also puts a guidance block, when to search before grep, into ~/.claude/CLAUDE.md. silica-core setup --list names the clients: claude, codex, cursor, windsurf, zed, cline, roo, continue, goose, opencode, openhands, gemini, antigravity, dsh, hermes, openclaw, agent-zero, claude-desktop, lmstudio, anythingllm and librechat; shell, python and generic print recipes for anything else. The server serves the folder the client opens in; --vault DIR or SILICA_VAULT fixes the root.

Every written block, and the Claude Code plugin, run silica-core mcp --retrieval local-hybrid: potion-retrieval-32M in the server process, index and vectors built in the background at start, the search lexical and dense: warming until they land. Nothing leaves the machine; the one download is the model, once. npx skills add kiycoh/silica-core installs the skills (the one that tells an agent when to reach for the tools, and five that explain, summarize, compare, schematize and diagram from the indexed documents), and nothing else. Shell recipes, Docker and the REPL are in public/harnesses.md.

How the Claude Code plugin works

In Claude Code the plugin is all you need: it brings its own server and the skills. The Install section above and silica-core setup claude are for other clients; with both, two servers serve the same folder.

Install

It needs uv on PATH, which starts the server.

claude plugin install silica-core --marketplace kiycoh/silica-core

That one step works on Claude Code 2.1.275 or later, and /plugin install silica-core --marketplace kiycoh/silica-core does the same inside a session. On an older client, add the marketplace first: claude plugin marketplace add kiycoh/silica-core, then claude plugin install silica-core@silica-core.

First run

1. Start Claude Code in the folder you want to search.
2. Wait for the first start. It is slower than the next ones: uv installs the packages and the server downloads its model, once.
3. Press Index above the prompt, or type /silica-init. Nothing is indexed until you do.
4. Ask a question about the folder. Claude searches it with silica_search. Until the vectors are built the search is lexical, and its replies say dense: warming.

Update

Refresh the marketplace, then the plugin. The new version loads in the next session.

claude plugin marketplace update silica-coreclaude plugin update silica-core@silica-core

What it runs, reads and downloads

The plugin is an MCP server plus a small mod in hooks/. Neither one sends your files, prompts or conversation anywhere.

• The server starts with uv run --frozen --project <plugin folder>. The plugin folder is ~/.claude/plugins/cache/silica-core/silica-core/<version>, with the version claude plugin list shows. The first time, uv installs the packages pinned in uv.lock from PyPI (and a Python build if the machine has no Python 3.11 or newer), and the server downloads the potion-retrieval-32M model from Hugging Face. Nothing else is downloaded.
• Indexing. In a folder that isn't indexed yet, the mod shows an Index button above the prompt; /silica-init does the same. Either one runs uv run --frozen --project <plugin folder> --extra mcp --extra dense silica-core init in that folder, which writes vault.yaml there (plus .silicaignore in a code repository) and builds the index under ~/.silica. Not here hides the button for that folder. Nothing is indexed until you ask.
• Search hints. In an indexed folder, when you ask a question that names no file or symbol, the mod adds one line asking Claude to try silica_search before grep. It also adds the search guidance to the system prompt, unless your CLAUDE.md already has it. The mod reads three environment variables, CLAUDE_CONFIG_DIR, HOME and USERPROFILE, only to find that CLAUDE.md and to skip your home folder.
• Docs upkeep. In an indexed folder with a docs/ folder, the mod helps Claude keep the docs in step with the code. It asks; Claude decides, and no write is ever refused.
  • After a write worth recording (a new file, a manifest, 30 changed lines in a turn, or a file an ADR lists), Claude gets one reminder: bring docs/ up to date, or say there is nothing to record.
  • When a turn that wrote under docs/ ends, the mod checks those files for links and code paths that lead nowhere, two ADRs with one number, and an accepted ADR whose Decision changed. Claude fixes what it agrees is a defect or says why it is not; the check asks at most twice a turn.
  • At the start of an interactive session it reads docs/adr/ and docs/specs/ and runs git, then shows above the prompt how many records name what is not there and how many have files that changed since. /silica-docs lists them.
  • A record whose frontmatter has implementation: (implemented, partial, pending, draft, dropped or n/a) is held to it: implemented and partial name a commit or a path in implemented_in, pending and draft name none, partial and dropped carry an implementation_note.

On an older Claude Code

The Index button, /silica-init, the search hints and the docs upkeep come from the mod, which needs Claude Code 2.1.293 or later. An older client still runs the server and the skills. Index a folder from a terminal opened in it instead:

uv run --frozen --project <plugin folder> --extra mcp --extra dense silica-core init

When it does not work

• The silica tools are missing, or Claude Code says it could not connect to plugin:silica-core:silica-core. The server did not start; /mcp shows its state. The usual causes are uv missing from PATH and a first install that failed. Start the server by hand in the folder to read the error:

  bash

  uv run --frozen --project <plugin folder> --extra mcp --extra dense silica-core mcp --retrieval local-hybrid

  When all is well it prints serving 5 tools on stdio, waiting for a client; Ctrl+C ends it.

• No Index button. It never shows in your home folder or in /, which are too large to index whole. After Not here it stays hidden in that folder, and /silica-init still indexes it. On a client older than 2.1.293, see above.

• What this machine can read. silica-core doctor checks the install and the folder:

  bash

  uv run --frozen --project <plugin folder> --extra mcp --extra dense silica-core doctor

Uninstall

claude plugin uninstall silica-core@silica-core

The plugin leaves two things behind:

• vault.yaml, and .silicaignore in a code repository, in each folder you indexed;
• the indexes in ~/.silica/index/, one folder each.

Delete them by hand. An index deleted while the plugin is still installed is rebuilt the next time its folder is searched.

Notes

• What it reads: markdown, .txt, .rst and PDFs with a text layer directly, one PDF page per section; DOCX, EPUB, FB2, RTF, XLS and ODF converted with no extra; scanned PDFs, images, PPTX and XLSX through silica-core import with MinerU; audio and video with ffmpeg plus SILICA_STT_BASE_URL; CSV readable by line, excluded from search. In a source tree the code lane adds source files and their json, yaml, toml, cfg and ini. silica-core doctor says which lanes this machine has.
• The dense leg: section embeddings that catch a paraphrase sharing no rare word with the answer. uv tool install stays lexical until silica-core index --embed, with the [dense] extra's local model or any OpenAI-compatible /v1/embeddings endpoint. Text leaves the machine only for a remote endpoint, and only after silica-core index --embed --allow-remote grants that host once. Variables and reply states in TOOLS.md, the ollama recipe in public/harnesses.md.
• More surfaces: silica-core mcp --extended adds the wikilink tools; silica-core connect (extra [connect]) hosts the bridge the Obsidian plugin dials into, so writes land through the vault API while the app is open; silica-core repl runs a small reference agent over the same tools, the one surface that needs a model (SILICA_MODEL).
• Not in the core: no memory lane, prompt injection, summaries or undo journal. Undo is git.

License

MIT. See LICENSE.