Semlith

A fast local vector store and code graph for AI agents — index your files once, keep it current as you save, and answer questions across all of it in milliseconds without leaving the machine.

What this is

An agent that needs to know something about a large corpus has two bad options: read everything, which is expensive and mostly irrelevant, or guess which file to open, which is usually wrong. What it wants is the two or three paragraphs that actually answer the question.

Semlith finds those paragraphs. Point it at your code, notes, PDFs, Office documents and notebooks; it reads each as the text a person would see, splits it into chunks, and builds two indexes over them.

A vector index, in plain terms

A model reads each chunk and turns it into a list of numbers — a few hundred of them — positioned so that chunks about the same thing end up near each other, whatever words they used. "Retries use full jitter" and "how does the backoff work" land close together without sharing a single term. Searching is then arithmetic: the question becomes a list of numbers by the same model, and the nearest chunks come back. The expensive half happens once, when a file is indexed, so semlith is built for a specific shape: indexing may be slow; querying may not be.

Vectors alone are weak at exact names — every constant in a codebase embeds to roughly the same place — so every query also runs the literal terms through a keyword index and fuses the two rankings. EMBED_BATCH and how does retry backoff work both land on the right chunk.

A code graph, in plain terms

The same indexing pass parses every source file and writes down two things: a node for each definition it finds — a function, a class, a method, a heading in a Markdown file, a key in a YAML one — and an edge for each relationship between two of them. This file defines that name; this function calls that one; this module imports that one; this re-export stands for that definition. It is extracted on the same changed-file pass that re-embeds the file, so there is no build step and no artifact that can go stale against your working tree.

Why the two together

Grep finds a string. A hosted embedding service finds text that reads like your question, and sends your code to somebody else's machine to do it. Neither answers what calls this, what would break if I changed it, or where is the thing that does this, called something I would never have guessed.

Semlith answers all three, locally. A search asks the vector index and the keyword index, then expands the best hits one hop through the graph and folds what it reaches into the same ranking — which catches the case neither list can reach alone: a concept spread across files that share no vocabulary. Every hit says which lists found it, so a result the graph alone reached reads as a neighbour of a match rather than as a match. Images go in too, embedded with CLIP beside the text. There are no API keys and no network at query time.

Install

One command. No Rust toolchain, no package manager, nothing installed first.

macOS and Linux

curl -fsSL https://raw.githubusercontent.com/semlith/semlith/main/install.sh | sh

Windows

irm https://raw.githubusercontent.com/semlith/semlith/main/install.ps1 | iex

The Windows line runs in PowerShell, and Windows PowerShell 5.1 is enough. The script picks the release for your machine, checks the download against the release's SHA256SUMS, unpacks it into ~/.semlith/bin, and hands off to semlith setup, which puts that directory on your PATH, pre-downloads the embedding model, registers semlith with the agents you say you use, and installs the daemon as a login service. setup is also the repair command, and --yes takes every default so a script can run it unattended. SEMLITH_VERSION pins a release by its tag, SEMLITH_HOME moves where it lands, SEMLITH_NO_SERVICE=1 skips the login service, and semlith upgrade swaps the binary for the newest release — never on its own, since semlith has no startup check, no timer and no update banner. Or build it with cargo install semlith, or take an archive from the releases page.

What a machine needs. 64-bit, and one of: Apple silicon macOS, Linux on x86_64 or aarch64, or Windows on x86_64. The Linux archives ship Microsoft's libonnxruntime.so beside the binary rather than linking it, so the pair needs nothing but glibc and libstdc++ — no OpenBLAS, no OpenSSL. Its floor is GLIBC_2.34 and GLIBCXX_3.4.22, measured over both files on every tagged build, which covers Debian 12, Ubuntu 22.04 LTS, RHEL 9 and Amazon Linux 2023. Intel macOS is not supported: ONNX Runtime no longer publishes osx-x86_64, so the embedding backend cannot link there.

Quick start

# Creates a store under ~/.semlith and downloads the model (~52 MB) once.
semlith index ~/notes ~/papers ./src

semlith search "how does the retry backoff work"   # ask it something
semlith stats                                      # what's in there
semlith start                                      # see it, and keep it current

1. 0.812  src/client.rs:120-158
   /// Retries use full jitter: the delay is uniform in [0, base * 2^attempt],
   /// capped at MAX_BACKOFF. ...

The path:start-end locator is usable as it stands: hand it to an editor.

Commands

semlith add fetches over https only, refuses redirects that leave https, caps the body at 32 MiB, writes only inside the store's own downloads/, and refuses everything under --airgap or to a private or loopback address, so a URL cannot read something inside your network. SEMLITH_ADD_ALLOW_PRIVATE=1 lifts that last rule, for a wiki on a LAN you own.

Where stores live

A new store goes in ~/.semlith/stores/<name>, and ~/.semlith/registry.json records which directories it covers, so semlith index ~/work/api then semlith index ~/work/cli leaves semlith mcp serving both with no path written anywhere.

With no flag, semlith resolves a store in this order: --store or SEMLITH_STORE, which always win; a .semlith beside the corpus, which always beats the home, so a setup predating the store home keeps working untouched; a registered store whose root is this directory or an ancestor of it; otherwise a new store in the home. semlith mcp and semlith start are the exception — with no flag they open every registered store, because a client stanza cannot know which directory your agent will be started in. search, stats, files and mcp read, so --store is repeatable; index, watch and forget write, so they take exactly one. semlith adopt ./.semlith moves an existing store into the home without re-embedding anything.

Keeping it current

semlith index is a snapshot of the moment it ran. semlith watch re-embeds a file when you save it: it starts with the same incremental pass index does, so anything that changed while it was down is caught up first, then waits on filesystem events rather than polling. Saves are batched until things go quiet for --debounce milliseconds, so a formatter rewriting a file three times costs one re-embed. It holds the store's write lock while it runs, so semlith index against that store exits non-zero and names the holder; searching is unaffected, and an MCP server already running picks the changes up without a restart.

The portal

semlith start is one process that owns every store you have indexed: it takes each store's write lock, watches its roots and re-embeds files as they are saved, and serves a page you can open.

$ semlith start
http://127.0.0.1:7365/?token=6f1c…
semlith: listening on 127.0.0.1:7365
semlith: opened api at /Users/you/.semlith/stores/api — watching 1 root(s)

That URL is printed once, on stdout. Everything else goes to stderr, and the token never appears there. Ten pages — Stores, Files, Index, Search, Graph, Agents, Ledger, Privacy, Doctor and About — each the same answer the terminal gives. The Graph page draws the symbols and edges the store holds, with a filter chip per edge kind and a confidence colour per edge. docs/portal.md documents every page, what each control does, and what each column, badge and number means.

It is not on the network. 127.0.0.1 is the only address it binds and there is no flag to change that. Every page and every /api/ route needs the per-run session token, sent in a Semlith-Token request header, and answers 401 with an empty body without it. The agent key is the other credential and it opens /mcp and nothing else, so a key sitting in a client's configuration file cannot rotate a token, adopt a store or start an upgrade. Every response carries a Content-Security-Policy allowing only 'self', no CORS header is sent, and every byte the page loads is compiled into the binary. --airgap makes that falsifiable: it refuses to download model weights at all and exits naming the cache path. docs/security.md is the full account, and the Privacy page checks each claim on the running daemon rather than restating it.

The daemon also ends the one-writer trade-off without weakening the rule: it is the writer, and while it runs semlith mcp finds it and forwards each call over loopback, so an agent's semlith_index and the watcher never collide.

Searching

semlith search "how does retry backoff work" --path 'src/http/**'
semlith search "how does retry backoff work" --ext rs --ext toml --lang rust
semlith search "how is the store lock taken" -s ../api/.semlith -s ../cli/.semlith

Each flag is repeatable. Repeats union, kinds intersect — --ext rs --ext toml means "Rust or TOML", while --path 'src/**' --ext md means "Markdown, under src". A leading ! excludes, after the inclusions of its own kind, so --path 'src/**' --path '!src/vendor/**' is everything under src but the vendored tree. The filter is applied before either half of the search picks its results, so asking for eight hits inside a subdirectory gets the eight best hits in that subdirectory rather than whatever survives filtering the eight best hits in the repository. Patterns are SQLite GLOB, so * crosses / and matching ignores case, and a filter that selects no indexed file says so rather than reporting that nothing in the corpus matched. Naming several stores searches all at once: every hit says which store it came from, -k is global, and merging happens on rank, so nothing compares two models' numbers.

semlith reads the shape of what you typed before it ranks anything. One token of identifier characters weights the keyword half twice; anything else is a question, and SEMLITH_RERANK=on gives a question a second opinion — a local 38 MB cross-encoder reads query and candidate together, which fusion never does. Two more questions of 77 at k=1, and 8.2 ms becomes 132 ms a search, so it is off by default. --prefer code lifts implementation over prose.

The code graph

All 46 languages --lang accepts carry graph edges, read from the same table the search filter reads, so the two cannot disagree. Fourteen of them are markup, data or configuration, where the structure is the symbol set — a YAML key, a Markdown heading, a Dockerfile stage, a SQL table, a CSS selector — and what those reference is files, so a change to a base image or a shared module has a blast radius you can ask about.

$ semlith neighbors acquire
callers (9)
  open_store via calls (extracted)  src/daemon.rs:645
  run via calls (inferred)  src/watch.rs:102
callees (8)
  read via calls (resolved)  src/daemon.rs:83
  write via calls (ambiguous) · 5 definitions
15 targets outside this store, not listed (--all)

$ semlith path search_in record_retrieval
search_in and record_retrieval are not connected within 6 hops by resolved
edges. Ambiguous names were not crossed; --all-edges walks them and labels it.

Every edge says how well it is supported. A call whose name, module or receiver the file also names was settled by the file itself and is extracted. Everything else is ranked against the definitions the store holds: one survivor is resolved, several are ambiguous and the row says how many rather than printing one of them as if it were the call, and a bare name match with nothing to rank is inferred. Trust the first two as answers, inferred as a hint and ambiguous as a question — four functions called get in four modules is the normal case in real code, and one row saying so beats four rows that each look like a call site.

A path walks definitions, not names. Every hop has to leave from the definition it arrived at, so semlith path refuses by default to cross a name it cannot pin down; --all-edges walks them anyway and labels the answer a hypothesis rather than a finding. semlith read is the second half of a search — one span or one symbol, answered out of the store's own chunks rather than off disk, so it can only return what semlith was allowed to index — and semlith pattern asks what a regex cannot, with the grammars the graph uses.

Finding an image

.png, .jpg, .jpeg, .webp and .gif are embedded with CLIP ViT-B/32's vision encoder into a second vector space inside the store, and a text query goes through the matching text encoder — that pairing is the whole trick, and it is why there is one fixed pair rather than a choice of image model.

$ semlith search "the architecture diagram with the queue in it"
1. 0.331  i   docs/design/pipeline.png:1280x720 px

It is not OCR. An image is matched by what it depicts, so a photograph of a whiteboard finds "a whiteboard covered in boxes and arrows" and a screenshot dense with text ranks poorly against the words in it. The model files are fetched on the first image a store indexes, so a corpus with no pictures never downloads them.

The retrieval ledger

Every retrieval goes into the store it came from — the query, the client that asked, the session, how many hits came back, and what the agent read — whether it came from an agent over stdio, from the daemon's /mcp endpoint, from the command line or from the portal.

$ semlith ledger --last 3
20:14:31 d20345  claude-code      8 hits      6 ms  where is the writer lock taken

Each row carries the hash of the row before it, so an edited or removed row is detectable rather than merely unlikely — an audit record rather than a log file, and semlith ledger --verify names the first row that does not verify and prints what the ledger adds up to. Recording is on by default and local: the rows never leave the store, erasing every row is one DELETE against a SQLite file you already own, --no-ledger stops a session and SEMLITH_LEDGER=0 stops a machine. It needs no licence key, now or ever.

What it saved, on this repository

Ask semlith brief all 107 questions of this repository's own retrieval harness against a store of src/, then run semlith ledger --verify: 3 982 tokens per answered question is what the agent was sent, 105 132 is what reading the 4.1 files those answers named would have cost whole — 26×, at 100 % coverage, counted by the store's own tokenizer rather than estimated. It is an upper bound: a file two answers both name is counted twice, where one real read would have served both. The command reproduces it against any store you have.

Using it from an agent

semlith mcp speaks MCP over stdio, and semlith start answers the same sixteen tools over HTTP at /mcp:

The write tools take the store's lock for the call and give it back; a store another process is writing comes back as a tool error naming the holder rather than a corrupted index. Indexing a large tree takes longer than a client will wait, so semlith_index works to a time budget and continues where it left off. A bare semlith mcp opens every store in the registry, so an agent asks one question across repositories and indexing a second needs no config edit. semlith implements MCP 2026-07-28, 2025-11-25, 2025-06-18 and 2024-11-05, each with a session in tests/mcp.rs proving it.

semlith setup registers semlith in every client that has a registration command, at the scope that means every project; semlith doctor says which it could not and what to run for them. docs/clients.md holds the stanzas for all 27 and the HTTP transport, and tests/clients.rs launches each.

A server that is silently absent does not exist. setup installs the daemon as a login service — launchd agent, systemd user unit, logon task — so it answers before any client asks; semlith start --no-service removes it. semlith doctor asks whether each client can actually reach it: it names the first step that failed and the command that shows it, repairs a registration that cannot launch, and catches what nothing else does — a server registered at user scope and switched off for one directory, which every check run from elsewhere calls healthy. --brief is one line and an exit code for a shell prompt or a session-start hook, and docs/clients.md has that snippet.

What gets indexed

Everything under the given paths except files ignored by .gitignore, hidden files, binaries (a NUL byte in the first 8 KiB, the five image formats aside), files over 8 MiB, an archive that decompresses to more than 32 MiB of text, and anything under a .semlith directory. A file that fails a cap or cannot be read is counted in the run's skipped total and the run carries on. What is left is read as the text a person opening the file would see, decided by the extension before anything looks at the bytes — which is what lets a .docx be read at all, since it is a ZIP archive the binary check would reject. Thirteen formats have a reader of their own, and where one has divisions a line number cannot express, a marker line names the slide, sheet or cell. Everything else is read as UTF-8, in line-aligned chunks of up to 800 characters with two lines of overlap. What the model is shown is more — a Markdown chunk carries its heading path, a code chunk the definition it sits inside — while the stored bytes stay the file's; an upgrade that changes that re-embeds the store once.

How it works

files ──chunk──> text ──embed──> vectors ──quantize──> index/*.tvim  (turbovec)
                  │
                  └──────────────────────────────────> store.db      (SQLite)

query ──embed──> vector ──search shards──> chunk ids ──lookup store.db──> excerpts

A store holds index/ — the turbovec index, shards of 65536 quantized vectors keyed by chunk id — and store.db, the SQLite database holding chunk text, paths, line spans, symbols, edges, the ledger and the content hashes that make re-indexing incremental. Sharding lets a search hold part of the corpus, a save rewrite one shard, and a long run checkpoint as it goes. Embeddings default to granite-embedding-small-english-r2 at int8, 384 dimensions, ~52 MB, on CPU via ONNX Runtime; the model is fixed when the store is created, because vectors from two models are not comparable. docs/architecture.md is the full account.

The numbers

Two kinds, kept apart because they go stale differently. Coverage is read out of the code and asserted by tests/readme.rs, which fails the build if one of these drifts from its source:

Measured, on a 4P+4E Apple Silicon laptop, with what reproduces each one:

Peak memory does not grow with the corpus — 105k chunks is 85 times the work of 1.2k for slightly less memory — so plan for roughly 600 MB whatever you point it at. Query latency does grow: the index scan is linear. docs/performance.md has the full tables.

Known limits

• One writer per store. A second index run against a store already being indexed exits with an error naming the process that holds it.
• First-time indexing is bound by transformer speed on CPU, at roughly 23 chunks/sec. Later runs touch only what changed.
• A store larger than SEMLITH_INDEX_MEMORY reads shards back from disk on every query. The bound is the point — a corpus larger than memory is searchable at all — but if your store fits, raising the budget is free speed.
• The default model is English-only and is fixed when a store is created. Image search is not OCR, and the CLIP pair behind it is fixed.
• Generated and vendored directories are not indexed: node_modules and its kind always, target/build/dist/vendor when their manifest sits beside them. SEMLITH_DEFAULT_IGNORES=0 indexes them anyway.
• Search filters are SQLite GLOB: no regex, though a leading ! excludes. --lang maps a fixed table of extensions and never reads contents.
• Rescoring is off by default and reads one store's own list, so multi-store search is still a merge rather than a joint ranking.
• Nothing goes looking for stores on the filesystem, nothing is code-signed, there is no ARM64 Windows or Intel macOS build, and semlith upgrade only replaces a binary in ~/.semlith/bin.

Documentation

docs/portal.md covers every page of the portal, every control, and the concepts behind the graph and the search list. docs/clients.md holds the configuration stanzas for 27 agent clients and the HTTP transport. docs/architecture.md is how the pieces fit together and why, docs/performance.md every measured number with its command and its date, docs/models.md the embedding models and how to choose one, and docs/security.md the threat model and what is on the wire. docs/compatibility.md says what is a contract and what is free to change under you, including what a 0.x version number does and does not promise; CHANGELOG.md says what changed.

Contributing

Contributions are welcome. CONTRIBUTING.md covers the checks CI runs, how the code is laid out, and what is deliberately out of scope; AGENTS.md is the same ground for a coding agent. Everyone participating follows the Code of Conduct. Found a security problem? Please read SECURITY.md rather than open an issue.

Prior art

Semlith's vector index is turbovec, by Ryan Codrai, under the MIT licence. It implements TurboQuant, from "TurboQuant: Online Vector Quantization with Near-optimal Distortion Rate" by Amir Zandieh, Majid Daliri, Majid Hadian and Vahab Mirrokni.

Quantizing a vector means keeping it in far fewer bits than it arrived in, which is what lets a million chunks be searched from memory. Most quantizers learn how from the data, so they need a representative sample of the corpus before they can compress any of it. TurboQuant is data-oblivious: it rotates each vector randomly and quantizes each coordinate on its own, with no sample and no training pass.

That is what an index refreshed on every file save needs. Nothing is gathered before the first file is indexed, nothing is rebuilt as the corpus grows, and a vector added is a vector searchable.

License

Apache-2.0. See LICENSE and NOTICE.

Note that semlith downloads embedding model weights at runtime; those are covered by their own licenses. The default, ibm-granite/granite-embedding-small-english-r2, is Apache-2.0, and the CLIP ViT-B/32 pair a store fetches once it holds an image carries its own too.