indexio

indexio is a code search engine for AI coding agents. It indexes all the repositories of an organization one time. It answers a query in milliseconds. It gives the index to agents as a tool through the Model Context Protocol (MCP) and through an HTTP API.

indexio is one binary, written in Rust. It does not need a database or an external service. The index is a set of files in one data directory. You can copy that directory to another machine.

Let your agent install it

Paste the block below to Claude Code, Cursor, Codex or any coding agent that can run shell commands. It installs indexio, indexes your code, registers the MCP server and verifies the result. Replace ~/code with the folder that holds your repositories.

Install indexio (https://github.com/IOServicesLabs/indexio) on this machine and connect it
to me. Do these steps in order and stop at the first failure with the exact error.

1. Install the binary.
   - Linux or macOS:  curl -fsSL https://raw.githubusercontent.com/IOServicesLabs/indexio/main/install.sh | sh
   - Windows (PowerShell):  irm https://raw.githubusercontent.com/IOServicesLabs/indexio/main/install.ps1 | iex
   - If neither works, use `pip install indexio-cli`, `npm install -g indexio`, or `cargo install --git https://github.com/IOServicesLabs/indexio indexio`.
   The binary lands in ~/.local/bin (Linux, macOS) or %LOCALAPPDATA%\Programs\indexio (Windows).
   If `indexio --version` is not found afterwards, add that folder to PATH and open a new shell.
   `git` must be on PATH.

2. Index my code:  indexio add ~/code
   This registers every git repository under the folder at any depth and builds the index.
   Nothing is uploaded; the index lives in ~/.indexio.

3. Register the MCP server with the agent you are.
   - Claude Code:  indexio setup claude --claude-md ~/.claude/CLAUDE.md
     then  indexio hook install
     (the hooks route file reads and greps through the index; scripts and builds run as before)
   - Any other MCP client: add this server to its MCP configuration and restart the client:
       command: indexio   args: ["mcp"]
     Use the absolute path of the binary if the client does not search PATH.

4. Verify. All four must succeed:
   - indexio --version                  prints a version
   - indexio stats                      lists the repositories and a file count above zero
   - indexio search "TODO" --limit 3    returns hits from my code
   - indexio usage                      prints a report (it is empty until I use the tools)

5. Tell me what was installed, where the data directory is, which repositories were
   indexed, and that I must restart my agent session so it picks up the new MCP server.
   Do not modify any file inside my repositories.

What the agent gets afterwards: code_search, code_grep, find_symbol, who_calls, file_outline, read_span, impact_of_symbol, impact_of_diff and recall as tools, answered from the index in milliseconds. The tools table describes each one.

Install

Pick one. Each one gives you the indexio command.

The scripts and the npm package download the binary of the latest release for your OS and CPU and check its SHA-256. The pip wheels carry the binary inside them, one wheel per platform. The pip package is called indexio-cli because indexio on PyPI belongs to an unrelated project; the command it installs is indexio. The container image works with no install at all: see Deploy with Docker. git must be on the PATH. No service, no database and no model download is necessary.

Upgrade

Run the same install command again. The index in ~/.indexio stays, and you do not index again.

Then do two more steps:

1. Run indexio hook install. It adds the hooks that the new version brings and repairs the others. It keeps your own hooks.
2. Restart your agent sessions. A running session keeps its indexio server until it restarts.

Running sessions do not stop you from upgrading:

• The two scripts replace the binary while sessions use it. On Windows, install.ps1 moves the running indexio.exe to indexio.old.exe and copies the new one in.
• On Windows, npm and pip try to overwrite the binary in place, and Windows does not allow that while it runs. Close your agent sessions first, or use the script.
• Sessions that still run the old version can read an index that the new version wrote.
• The first new server does its one-time work in the background: it embeds files that have no vectors and it writes session cards. Calls are not blocked.

Quick start

Three commands. The third one is only for Claude Code.

indexio add ~/code            # 1. index every git repository under a folder
indexio search parse_config   # 2. search it (add --mode hybrid for a question in words)
indexio setup claude          # 3. register the MCP server with Claude Code

Then restart Claude Code. Its sessions now have the indexio tools. Two optional commands make the savings larger:

indexio hook install          # reads and greps of indexed files go through the index
indexio sync                  # run from cron or a timer to keep the index current

indexio stats shows what is indexed. indexio usage shows the tokens the index served against what the built-in tools would have returned.

All data goes into one directory: --data-dir, $INDEXIO_DATA_DIR, or ~/.indexio.

Contents

1. Let your agent install it
2. What indexio does
3. Add sources
4. Keep the index current
5. Embeddings
6. What is never indexed
7. Secure the HTTP API
8. Team indexing: live worktree overlays
9. Enterprise setup
10. Use indexio with Claude Code
11. Token savings, measured
12. Impact analysis
13. Use indexio from other tools
14. Command reference
15. Environment variables
16. Deploy with Docker
17. Architecture
18. Measured performance
19. Limits
20. Development and releases

What indexio does

indexio answers three kinds of question about the code of an organization.

indexio also knows the definitions and the call graph of the code. It can tell you where a symbol is defined, who calls it, and what breaks if you change it.

Add sources

Each add indexes the source immediately and builds the semantic plane.

indexio add ~/code                             # every git repository under the folder, at any depth
indexio add /srv/checkouts/legacy-monolith     # a folder without git: indexed as-is
indexio add github:my-org                      # a GitHub organization or user
indexio add github:my-org/payments             # one GitHub repository
indexio add azdo:my-org/Platform               # an Azure DevOps project
indexio add https://gitlab.example.com/g/r.git # any git host

Search:

indexio search parse_config
indexio search "how is backpressure applied" --mode hybrid

Serve the index to agents:

indexio mcp                           # MCP over stdio
indexio serve                         # HTTP API on http://127.0.0.1:7717

indexio remembers each source in <data-dir>/sources.json. indexio sources lists the sources and the registered repositories. indexio remove <source> forgets a source.

Useful flags for add: --limit 20 (trial run on a large organization), --include-forks, --include-archived, --full-clone, --dest DIR (where remote clones go), --no-embed, --exclude PATH, --pdf-text.

Folders with repositories and other files. A folder often holds git repositories and files that are not in any repository: notes, specs, exports, PDFs. indexio add indexes each repository as a repository, and the other files as one more repository with the folder's name:

projectA/                     indexio add ~/projectA
├── backend/   (git)    →     repository "backend"
├── frontend/  (git)    →     repository "frontend"
├── docs/notes.md       →     repository "projectA": the contents
├── docs/spec.pdf       →     repository "projectA": the name only
└── old-copy/           →     left out with --exclude old-copy

• Text files are indexed by contents, up to the size limit (256 KiB for text, 4 MiB for code).
• Documents (PDF, Word, Excel, PowerPoint, OpenDocument, RTF, EPUB) and text files over the limit are indexed by name only. list_files and a search for words of the name find them. read_span on one says that its contents are not indexed; read the file itself. The hooks let a Read of such a file through.
• --pdf-text indexes the text layer of these PDFs instead of their name. A PDF that was exported from a document (Word, Google Docs, a browser) has one, so a search finds words inside it. A scanned PDF has no text layer and keeps its name-only entry: indexio does no OCR. The extracted text has the text size limit. A PDF over 64 MiB, or one that takes longer than 20 seconds to read, keeps its name-only entry. The option is remembered with the source.
• Images, media, archives and other binary files are not indexed.
• --exclude PATH (repeatable, relative to the folder) keeps a folder out: it is not a repository and its files are not indexed. Excludes are remembered with the source and accumulate when you run add again.
• A folder that is registered on its own is not indexed a second time.

Credentials. indexio reads credentials from the environment only: GITHUB_TOKEN (or GH_TOKEN) and AZDO_TOKEN (or AZURE_DEVOPS_EXT_PAT, SYSTEM_ACCESSTOKEN). It sends them to the listing APIs and to git as an authorization header. It never puts them in a clone URL, in a log, or in .git/config. Public repositories do not need a token.

Keep the index current

Run indexio sync from cron or a timer, for example every 15 minutes. Each run is incremental:

• New repositories are cloned.
• Changed git repositories are delta-indexed by commit.
• Changed plain folders are delta-indexed by content hash.
• New and changed chunks are embedded. All other chunks are cache hits.

A folder tree of 156 repositories and 17,530 files syncs as a no-op in 11 s.

A running indexio mcp server does more on its own:

• It watches the repository the session works in. It re-indexes the working tree before each call when files changed. Uncommitted and untracked edits are searchable at once; their embeddings follow on a background thread within a few hundred milliseconds.
• Every 10 minutes it probes the other repositories for a moved HEAD and re-indexes the ones that moved, and re-indexes changed plain folders by content (after the first pass, an unchanged file costs one stat).
• A session that starts before its folder is registered adopts the repository within one minute of indexio add. No restart is necessary.

Embeddings

The built-in model

The default embedder is Random Indexing (rindex). It is a semantic model that indexio builds in-process from your own code, on the CPU, in one streaming pass. It needs no training infrastructure, no download and no GPU. It learns the vocabulary of your organization: internal service names, code names and APIs that no pretrained model knows.

Each new chunk is an incremental update, so indexio sync stays cheap.

Measured on 20 hard concept queries (bench/): hybrid recall@5 is 60 % and MRR is 0.397. Lexical search alone gives 5 % and 0.050 on the same queries.

An optional neural endpoint

For maximum retrieval quality, point indexio at any OpenAI-compatible embeddings endpoint, for example Qwen3-Embedding on vLLM or TEI. The two model namespaces coexist.

export INDEXIO_EMBED_BASE=http://embed.internal.example:8080
export INDEXIO_EMBED_MODEL=Qwen/Qwen3-Embedding-8B
export INDEXIO_EMBED_DIM=1024
export INDEXIO_EMBED_KEY=...                                    # only if the gateway needs it
indexio embed                                                   # builds vec/<model-id>.*.civec

Embeddings are content-addressed by (chunk hash, model id). Two repositories that share a file share its embedding. Duplicate chunks across an organization cost nothing extra.

An optional reranker

Add a reranker endpoint, for example Qwen3-Reranker on TEI or vLLM. indexio uses it when a query asks for it: indexio search --mode hybrid --rerank, rerank=1 over HTTP, or rerank: true over MCP. Without an endpoint, --rerank has no effect.

export INDEXIO_RERANK_BASE=http://rerank.internal.example:8081
export INDEXIO_RERANK_MODEL=Qwen/Qwen3-Reranker-8B
export INDEXIO_RERANK_KEY=...

What is never indexed

• Files without a known code, document, configuration, script or data extension, such as databases, images, archives and compiled output.
• Binary content: a NUL byte in the first 8 KiB skips the file. Files over 4 MiB, and text files over 256 KiB. In a plain folder, these files and documents (PDF, Office) are indexed by name only (see Add sources).
• Build output, dependency and cache folders (node_modules, target, dist, vendor, any folder with a CACHEDIR.TAG), git-ignored files, hidden folders except the configuration ones (.github, .cargo, .vscode, .devcontainer …), lock, minified and source-map files.
• Credentials: .env files, private keys and certificates (pem, key, p12, pfx, jks, gpg …), .netrc, .npmrc, Terraform state. A credential file indexed by an earlier version is removed by the next sync. .env.example and *.pub are kept.

The session transcripts and run logs that recall searches are redacted before they are stored: values of secret-looking settings, passwords in URLs, API keys, bearer tokens, JWTs and private-key blocks are replaced with <redacted>.

Secure the HTTP API

indexio serve binds to the loopback address by default.

indexio serve --auth-token $(openssl rand -hex 32)               # one bearer token

For per-token repository access, use an ACL file:

cat > acl.json <<'EOF'
{"tokens":{"indexio-reader":{"allow":["team-*","core"]},"indexio-admin":{"allow":["*"]}}}
EOF
indexio serve --acl-file acl.json

With an ACL file:

• An unknown token gets HTTP 401.
• Hits outside the allowed patterns are removed from /search, /symbol and /calls.
• Admin routes need a token with allow: ["*"]. Other tokens get HTTP 403.
• GET /health is always open.

Caution. A bind address other than loopback (--bind 0.0.0.0) is refused unless you also set --auth-token, $INDEXIO_AUTH_TOKEN or --acl-file. The MCP server over stdio runs as the local user and has no authentication by design. Put a network-facing MCP server behind your own gateway.

Team indexing: live worktree overlays

indexio serve can layer every developer's uncommitted changes on top of the shared index, so an agent answering you sees your working tree — edits, untracked files, deletions — while everyone else keeps seeing the pushed state. Nothing to install on the developer machine beyond a shell hook in the agent harness: no indexio client.

How it works

1. The server indexes the pushed repositories (the usual add + sync).
2. A PreToolUse hook in the agent harness runs integrations/claude-code/indexio-team-sync.sh before every indexio tool call. The script diffs the working tree (untracked files included) against the merge-base with the remote default branch and POSTs the patch to /team/worktree.
3. The server applies the patch into a small overlay shard keyed by the caller's user name, layered over the base shards: changed paths shadow the base index, deleted paths are hidden, everything else reads from the shared index. Applying uses git plumbing on a scratch index — no checkouts, no worktrees.
4. A hash of the last accepted patch is kept on disk, so repeated calls with unchanged work cost nothing. The hook prints nothing and always exits 0: it can never block a tool call or pollute the agent's context.

Overlays expire after INDEXIO_TEAM_TTL_DAYS (default 7) without an update.

Server setup

Serve with an ACL file whose tokens carry a "user" — that name keys the overlay:

cat > acl.json <<'EOF'
{"tokens":{
  "tok-alice":{"allow":["*"],"user":"alice"},
  "tok-bob":  {"allow":["*"],"user":"bob"},
  "tok-ci":   {"allow":["*"]}
}}
EOF
indexio serve --acl-file acl.json --bind 0.0.0.0

A token without "user" works for reading but has no overlay (CI, above). With a single --auth-token instead of an ACL file, clients pick their user with the X-Indexio-User header.

Developer setup

indexio setup claude --team-sync              # writes the hook script, prints the entry
export INDEXIO_URL=https://indexio.example.com
export INDEXIO_TOKEN=tok-alice

setup claude --team-sync writes the hook script into the Claude config dir and prints the PreToolUse entry for settings.json — matcher mcp__indexio__.*, so the sync runs right before any indexio tool call. With one shared token instead of per-user tokens, also set INDEXIO_USER to the name to act as.

What is enforced server-side

• Credential paths (Lang::is_secret_path) are never accepted into an overlay, and neither are patches over 32 MiB.
• ACL allow patterns filter what each user reads — on the documents themselves for MCP (rendered text cannot be un-shown), as hit-filtering on the REST API.
• Overlay user names are constrained to [A-Za-z0-9._@-], no leading dot, so overlay state stays path-safe (SSO identities are usually emails).

Limits

• Overlays are lexical planes. Vector search ranks the base content; edits to tracked files surface through every tool, while brand-new untracked files and deletions are visible to the lexical, symbol and outline tools.
• The base must be a commit the server has (the merge-base with origin/HEAD, else origin/main, origin/master, or the upstream branch), otherwise the upload is refused with HTTP 409 and retried on the next call. The server fetches the origin itself, rate-limited to once a minute.
• The hook ships tuned for Claude Code; the PreToolUse contract is the one other harnesses are converging on, but only Claude Code is tested.

Enterprise setup

Everything above runs on one machine. The same binary scales to a team server or an organization-wide deployment; the moving parts are the network edge and authentication.

Inside the network (LAN / VPN)

The simplest topology: one indexio server on an internal host, bound to a private interface; TLS optional on a trusted network.

indexio serve --bind 10.0.0.5 --acl-file acl.json

Developers aim their team-sync hook at it with INDEXIO_URL + INDEXIO_TOKEN. Start with an ACL file; move to SSO (below) when handing out tokens becomes the chore.

Facing the internet

The server speaks plain HTTP and refuses to bind wide without credentials, so put it behind a reverse proxy that terminates TLS and forwards to the loopback port. A minimal Caddy site:

indexio.example.com {
	reverse_proxy 127.0.0.1:7717
}

Then serve with SSO rather than static tokens: a short-lived identity token beats a long-lived bearer on a laptop.

SSO with an OIDC provider (Entra ID, Google, Keycloak)

--oidc-issuer + --oidc-audience replace the static-token modes. The server discovers the provider at <issuer>/.well-known/openid-configuration, caches its JWKS, and validates every bearer token (RS256, issuer, audience, expiry) before looking the identity up — fail closed:

cat > users.json <<'EOF'
{"users":{
  "alice@corp.example":{"allow":["*"],"user":"alice"},
  "bob@corp.example":{"allow":["payments-*"]}
}}
EOF
indexio serve \
  --oidc-issuer https://login.microsoftonline.com/<tenant-id>/v2.0 \
  --oidc-audience <application-id-uri> \
  --acl-file users.json --bind 0.0.0.0

• The identity is the token's email claim (else sub). An identity not present in users.json gets HTTP 401: provisioning is your existing directory, mirrored into this file by hand or by a sync job.
• allow works exactly like the token ACL; /admin still needs *. "user" sets the team-overlay name — without it the email is used.
• IdP specifics. Entra ID: an app registration with an exposed API; the audience is the Application ID URI. Google Workspace: a Web application OAuth client; the audience is the client ID. Keycloak: a confidential client in your realm; the audience is the client ID and the issuer https://<host>/realms/<realm>.
• Signing keys rotate without a restart: an unknown kid refetches the JWKS on demand.
• OIDC mode supersedes --auth-token/INDEXIO_AUTH_TOKEN; leave them unset. --oidc-audience requires --oidc-issuer.

Try it: Google Workspace in ten minutes

The exact flow, verified end-to-end against a live server on 2026-09-27.

1. Google Cloud console: create a project (indexio-pilot, say).

2. APIs & Services → OAuth consent screen: External; app name indexio pilot; scopes openid and email; add your own Google account under Test users — while the app is in "Testing", only test users can consent. This is the step everyone forgets.

3. Credentials → Create OAuth client ID → Web application: add authorized redirect URI https://developers.google.com/oauthplayground.

4. Mint a real ID token at https://developers.google.com/oauthplayground: gear icon → "Use your own OAuth credentials" → paste the client ID and secret → scope openid email → Authorize APIs → consent → Exchange authorization code for tokens → copy the id_token.

5. Serve with the client ID as the audience and your email in the users file:

   bash

   Copy

   cat > users.json <<'EOF'
   {"users":{"you@corp.example":{"allow":["*"],"user":"pilot-you"}}}
   EOF
   indexio serve --bind 0.0.0.0 \
     --oidc-issuer https://accounts.google.com \
     --oidc-audience <client-id>.apps.googleusercontent.com \
     --acl-file users.json
   

6. Smoke test from anywhere:

   Terminal

   Copy

   curl -H "Authorization: Bearer $ID_TOKEN" http://indexio.example.com:7717/search?q=parse
   # 200 with the token; 401 without. The token lives one hour — re-run
   # the playground exchange for a fresh one.
   

Beyond the playground, anything that can run the OAuth consent flow can produce a bearer the server accepts: an IDE plugin, a small login page in front of the server, or a CI job.

GitHub

GitHub is not a general OIDC provider for your own API, but two patterns cover it:

• GitHub Actions → indexio is OIDC already. A job with permissions: id-token: write requests a JWT (issuer https://token.actions.githubusercontent.com, audience of your choosing) and hands it to indexio clients as the bearer token. The server validates it like any OIDC token:

  bash

  Copy

  indexio serve --oidc-issuer https://token.actions.githubusercontent.com \
    --oidc-audience indexio --acl-file users.json
  

  CI machines hold no static token, and the allow list in users.json scopes what each workflow may read.

• Humans with GitHub accounts. Put an OIDC gateway in front (oauth2-proxy configured for GitHub) and keep ACL-file tokens between gateway and indexio, or move human access to Entra ID / Google, where directory-backed provisioning belongs.

Humans vs agents

Keep the two populations on different credentials: humans on SSO short-lived tokens, agents and CI on ACL-file tokens scoped to the repositories they touch (allow: ["payments-*"]). Revoking a human is disabling their directory account; revoking an agent is deleting one line of the ACL file.

Use indexio with Claude Code

indexio speaks MCP over stdio. This is the native tool interface of Claude Code, of the Claude Agent SDK and of most coding agents.

Register the server

Do one of these:

• Run indexio setup claude. It runs claude mcp add for this binary and data directory, and it prints the guidance block for your CLAUDE.md. Add --claude-md ~/.claude/CLAUDE.md to append the block.

• Run claude mcp add indexio -- /usr/local/bin/indexio mcp --data-dir /var/lib/ciindex.

• Commit a .mcp.json to the project:

  config.json

  Copy

  {
    "mcpServers": {
      "indexio": {
        "command": "/usr/local/bin/indexio",
        "args": ["mcp", "--data-dir", "/var/lib/ciindex"]
      }
    }
  }
  

Install the hooks

indexio hook install

This writes four Claude Code hooks into ~/.claude/settings.json:

The Bash hook also routes scripts and builds (python, node, npm, pytest, go, make …) through indexio run, which keeps a long output out of the context: the first lines, the error lines and the last lines are returned with a runs:<repo>/<log> pointer, and the full output stays searchable for 30 days.

To run a refused command as typed, add # raw to it and send it again, or set INDEXIO_RAW=1.

The tools

The server tells Claude which built-in tool each indexio tool replaces, and which repositories are indexed. Claude then routes an identifier to lexical search and a question to hybrid search on its own. It reads a file by outline and span instead of whole.

Results are dense plain text: grouped repo:path and line: snippet rows, folded file lists, numbered spans. No scores, ranks or JSON punctuation. This costs 54 % fewer tokens than compact JSON for the same hits. Set INDEXIO_MCP_FORMAT=json for the JSON form.

Token savings, measured

Against the built-in tools, on the same tasks

bench/ab_readme.py runs the tasks a coding agent does through the built-in tools of Claude Code and through indexio, on the same repositories. Grep prints every match as path:line:text. Read prints the whole file, 2,000 lines at most. Glob prints one path per line. Tokens are counted with tiktoken. Three real repositories, 44 in the index, 10 symbols and 3 file types per repository, questions written by a model.

Where the built-in tool is cheaper, the difference is a few hundred tokens. Where it is expensive, it is expensive by orders of magnitude, because Read returns files and Grep returns every match of every word.

On real traffic

The server logs every call with the bytes it returned. Where the built-in tool has a mechanical equivalent, the server also logs what that tool would have returned:

index_stats ends with the last seven days across all sessions. indexio usage prints the same per tool and per repository. One day of real coding sessions on the author's machine: 423 compared calls, 220k tokens served where the built-in tools would have returned 596k, a reduction of 63 %. read_span alone: −71 %.

Impact analysis

indexio impact --symbol RateLimiter::acquire --depth 2     # transitive callers, all repositories
indexio impact --diff my-service                           # uncommitted working-tree changes
indexio impact --diff-file pr.patch --repo my-service      # a patch
indexio impact --file my-service:src/auth/token.rs         # every definition in a file, plus importers
indexio outline my-service:src/auth/token.rs               # definitions with line ranges
indexio span my-service:src/auth/token.rs 120:160          # exact lines

The walk is a breadth-first search over the reverse call graph that the index holds. It costs nothing at index time and answers in milliseconds. A patch is mapped to definitions with a tree-sitter pass over the changed files only. Changed files are excluded from the result. Their importers are found with a language-aware import query.

Edges are name-based. Foo::new and Bar::new share the node new. Each site carries its caller, path and symbol, so an agent can filter. Fan-out caps keep hub names bounded; truncated: true tells you when a cap fired.

The HTTP API has the same surface: GET /impact/symbol, POST /impact/diff, GET /outline, GET /span. All of them apply the ACL.

Use indexio from other tools

Any agent framework can use the HTTP API.

curl 'http://127.0.0.1:7717/search?q=auth%20token%20refresh&mode=hybrid&limit=10'
curl 'http://127.0.0.1:7717/symbol/RateLimiter'
curl 'http://127.0.0.1:7717/calls/RateLimiter::acquire'

A response is a JSON list of hits: repository, path, line, column, snippet, score.

Command reference

Each command accepts --data-dir DIR. The default is $INDEXIO_DATA_DIR, then ~/.indexio.

Index code

indexio add ~/code                          # every git repository under a folder
indexio add ~/notes                         # a folder without git: indexed as-is
indexio add github:my-org                   # a GitHub organization
indexio add github:my-org/payments          # one repository
indexio add azdo:my-org/Platform            # an Azure DevOps project
indexio add https://gitlab.example.com/g/r.git
indexio add github:my-org --limit 20 --no-embed     # trial run: 20 repositories, lexical only
indexio add github:my-org --dest /srv/clones        # where remote clones go
indexio index ~/code/one-repo --name one            # one repository, no source bookkeeping
indexio sources                             # sources and registered repositories
indexio remove github:my-org                # forget a source

Keep it current

indexio sync                                # pull, discover, delta re-index, embed. Run from cron.
indexio sync --no-embed                     # lexical plane only
indexio reindex --repo payments             # one repository, from HEAD
indexio reindex --repo payments --worktree  # from the working tree, uncommitted edits included
indexio reindex --all

Search

indexio search parse_config                                  # exact identifier
indexio search 'parse_config repo:payments lang:rust'        # filters: repo: lang: path: case:
indexio search '"token refresh"'                             # phrase
indexio search '/fn (parse|load)_config\(/'                  # regex
indexio search 'how is backpressure applied' --mode hybrid   # question
indexio search 'retry with exponential backoff' --mode semantic --limit 10
indexio search 'rate limiter' --mode hybrid --fusion combmnz # alternative fusion
indexio search 'rate limiter' --mode hybrid --rerank         # needs INDEXIO_RERANK_BASE
indexio search parse_config --json

Symbols and blast radius

indexio symbol parse_config                 # definitions
indexio calls parse_config                  # call sites
indexio impact --symbol parse_config        # transitive callers and importers, 2 hops
indexio impact --symbol parse_config --depth 3 --max-sites 1000
indexio impact --diff payments              # the uncommitted working tree
indexio impact --diff payments --base origin/main
git diff main | indexio impact --diff-file - --repo payments
indexio impact --file payments:src/config.rs
indexio impact --symbol parse_config --json

Read from the index

indexio outline payments:src/config.rs      # definitions with start and end lines
indexio span payments:src/config.rs 120     # the definition at line 120
indexio span payments:src/config.rs 120:160 # a range, 400 lines at most

Embeddings

indexio embed                               # embed every repository, incrementally
indexio embed --repo payments
indexio embed --all --rebuild-model         # retrain the built-in model from scratch
indexio embed --max-chars 800               # smaller chunks
indexio embcas-stats                        # embedding cache statistics
indexio embcas-stats --coverage             # per repository: indexed files without vectors

Serve

indexio mcp                                 # MCP over stdio
indexio mcp --repo payments                 # pin the session's repository
indexio serve                               # HTTP on 127.0.0.1:7717
indexio serve --port 8080 --auth-token $(openssl rand -hex 32)
indexio serve --bind 0.0.0.0 --auth-token "$TOKEN"          # beyond localhost: a token is mandatory
indexio serve --acl-file acl.json
indexio serve --oidc-issuer https://idp.example.com --oidc-audience indexio-api --acl-file users.json
# team worktree overlays: POST /team/worktree (see "Team indexing" above)

Agent setup

indexio setup claude
indexio setup claude --claude-md ~/.claude/CLAUDE.md
indexio setup claude --team-sync            # also install the team worktree-sync hook
indexio hook install
indexio hook install --print-only
indexio sessions                            # import Claude Code transcripts for recall
indexio sessions --project C--Users-me-code-payments

Run commands without filling the context

indexio run -- python scripts/probe.py --fast    # short output printed as is; long output stored + digested
indexio run -- npm test                          # the Bash hook does this rewrite for you
indexio run --cwd ~/code/payments -- pytest -q

A stored log is runs:<repo>/<stamp>-<command>.log: read_span it for the lines the digest left out, recall finds it later. Logs roll off after INDEXIO_RETAIN_DAYS.

Measure and maintain

indexio stats                               # repositories, files, shards, index size
indexio usage                               # last 7 days of MCP calls, against the built-in tools
indexio usage --days 1 --json
indexio compact                             # merge shards
indexio compact --vectors                   # also merge vector segments
indexio cas-stats

Environment variables

Deploy with Docker

The release workflow publishes ghcr.io/ioserviceslabs/indexio for linux/amd64 and linux/arm64. The image runs as an unprivileged user. The data directory is /data. git and CA certificates are included.

If you are indexing your own machine for your own agent, install the binary instead. The container is for a shared index that several people or machines query over HTTP. On your own laptop it costs you the Bash hooks, the instant working-tree refresh and a layer of path translation, and buys nothing. Use Install above. The rest of this section is for the shared case, and for trying indexio without installing anything.

Index a folder on this machine and search it, with nothing installed but Docker:

docker run --rm -v indexio-data:/data -v ~/code:/repos:ro ghcr.io/ioserviceslabs/indexio add /repos
docker run --rm -v indexio-data:/data ghcr.io/ioserviceslabs/indexio search parse_config
docker run --rm -v indexio-data:/data ghcr.io/ioserviceslabs/indexio stats

Serve the HTTP API:

docker run -d --name indexio -p 127.0.0.1:7717:7717 -v indexio-data:/data   -e INDEXIO_AUTH_TOKEN="$(openssl rand -hex 32)" ghcr.io/ioserviceslabs/indexio
curl -H "Authorization: Bearer $TOKEN" 'http://127.0.0.1:7717/search?q=parse_config'

Give the container to an agent as an MCP server (stdio through docker run -i):

claude mcp add indexio -- docker run -i --rm -v indexio-data:/data -v ~/code:/repos:ro ghcr.io/ioserviceslabs/indexio mcp

How the container indexes code on your machine

The container has no access to your disk beyond what you bind-mount into it. Two mounts do the work, and they are not symmetric:

indexio add /repos walks the mount, registers every git repository under it at any depth, and indexes each one. A folder with no git repository in it is indexed as a plain tree. Each repository is recorded in /data/repos/<name>.json with the path as the container sees it — /repos/my-service, never C:\Users\you\code\my-service. Results are repository-relative (my-service:src/main.rs), so searching is unaffected, but the host path is nowhere in the index.

Three consequences worth knowing before you build a large index:

• A container index and a host index are not interchangeable. If you point the host binary at a data directory built in a container, the recorded /repos/... paths do not exist on the host, so re-indexing and read_span on unindexed content fail. Pick one and stay with it, or keep two data directories.
• Freshness comes from the sync loop, not from a file watcher. indexio sync on a local folder re-discovers the repositories under the root and delta re-indexes whatever is on disk right now. It does not clone, pull, or write to your source — only the remote source kinds (github:, azdo:, a git URL) fetch anything. The sync service in docker-compose.yml runs that every 15 minutes.
• The auto-refresh does not survive the mount. indexio mcp normally watches the current repository and re-indexes the working tree in about 25 ms after an edit. Filesystem events do not cross a Docker Desktop bind mount from a Windows or macOS host reliably, so in a container treat the index as fresh to the last sync or refresh_index call, not to the last keystroke. This is the main reason to run the host binary next to an agent that is editing code.

The Bash hooks (indexio hook install) also need the host binary: they rewrite commands in your shell, which a container cannot see.

On Windows, generate the serve token in PowerShell rather than with the bash line above:

$bytes = New-Object byte[] 32
[System.Security.Cryptography.RandomNumberGenerator]::Fill($bytes)
$env:INDEXIO_AUTH_TOKEN = [System.BitConverter]::ToString($bytes).Replace('-','').ToLower()

The image sets INDEXIO_BIND=0.0.0.0, so serve refuses to start without INDEXIO_AUTH_TOKEN or --acl-file: an index of all your source is not something to publish unauthenticated. Do not "fix" that by setting INDEXIO_BIND=127.0.0.1 in the container — the service then binds the container's own loopback and published ports cannot reach it. Keep the bind at 0.0.0.0, set a token, and publish to 127.0.0.1:7717:7717 so only your machine can connect.

Continuously index one folder

Say the code lives in C:\codebuilds and you want it re-indexed on a timer, with an agent querying it over MCP. You need no auth token for this: the token guards serve, the HTTP API, and this setup does not run it.

Register the folder and build the index once. add records /repos as a persistent source, which is what later syncs re-read:

docker run --rm -v indexio-data:/data -v C:/codebuilds:/repos:ro `
  ghcr.io/ioserviceslabs/indexio add /repos

Then leave a container running that re-syncs on a loop. The image's entrypoint is the binary, so override it to get a shell:

docker run -d --name indexio-sync --restart unless-stopped `
  -v indexio-data:/data -v C:/codebuilds:/repos:ro `
  --entrypoint /bin/sh ghcr.io/ioserviceslabs/indexio `
  -c "while true; do indexio sync || true; sleep 900; done"

Point your agent at the same volume. The MCP server is stdio, so it needs no port and no token:

claude mcp add indexio -- docker run -i --rm -v indexio-data:/data -v C:/codebuilds:/repos:ro ghcr.io/ioserviceslabs/indexio mcp

Check it with docker run --rm -v indexio-data:/data ghcr.io/ioserviceslabs/indexio stats, which should list every repository found under C:\codebuilds.

Use forward slashes in the mount (C:/codebuilds), and make sure the drive is shared in Docker Desktop's file-sharing settings. Lower the sleep if 15 minutes is too coarse — but an edit is visible only after the next sync, so if you want the index to track your edits as you make them, run the host binary instead.

To use docker-compose.yml for the same thing, set the folder and start only the sync service:

$env:INDEXIO_REPOS = "C:/codebuilds"
docker compose up -d sync
docker compose exec sync indexio add /repos

Compose interpolates the whole file before it selects a service, so INDEXIO_AUTH_TOKEN must still be set for the file to parse even when you are not starting the indexio service. Set it as above, or use the plain docker run form.

docker-compose.yml runs two services on one volume:

• indexio: the HTTP API, published on localhost only.
• sync: indexio sync every 15 minutes. GITHUB_TOKEN and AZDO_TOKEN pass through.

1. Put the folders to index under ./repos.
2. Start the services: INDEXIO_AUTH_TOKEN=$(openssl rand -hex 32) docker compose up -d
3. Index the folders one time: docker compose exec sync indexio add /repos

The container binds 0.0.0.0. The binary refuses to start without INDEXIO_AUTH_TOKEN or an ACL file. docker build -t indexio . builds the same image from source.

Architecture

            ┌──────────────────────────── data dir ────────────────────────────┐
 git repos  │  shards/*.cidx   immutable mmap'd index shards (single file)      │
    │       │  cas/            global content-addressed store (blake3 keyed)    │
    ▼       │  embcas/         embedding CAS: (chunk-hash, model-id) → vector   │
 indexio-ingest  │  vec/*.civec     int8 vector segments + binary prescan            │
  git delta │  repos/*.json    per-repo indexing state (last commit)            │
    │       └──────────────────────────────────────────────────────────────────┘
    ▼
 Lexical plane                             Semantic plane
 ─────────────────────                     ──────────────────────────
 trigram inverted index                    tree-sitter chunking
 FST term dictionary, LEB128 postings      pluggable embedder (built-in model
 symbols + call edges (tree-sitter,          or any OpenAI-compatible endpoint)
 6 languages, AST discarded at once)       embedding CAS (org-wide dedup)
 query planner: required literals,         mmap'd binary prescan + int8 rescore
  galloping intersection, verify, BM25
            └─── indexio-query: RRF fusion → optional reranker ───┘
                                   │
                    CLI · HTTP (axum) · MCP (stdio JSON-RPC)

Five design decisions:

1. A trigram index, not a resident AST. indexio parses the AST, takes symbols, call edges and chunk boundaries from it, and discards it. A resident AST costs 20 to 50 times the text size. Trigram shards cost 1 to 3 times the corpus and answer in milliseconds.
2. A global content-addressed store. Extracted artifacts and embeddings are keyed by content hash across the organization. A fork, a vendored copy or a duplicated file is indexed and embedded one time.
3. Immutable mmap'd shards with tombstones. An index build writes new shards. A deletion is a bitmap tombstone. indexio compact merges shards in the background. Readers never block writers.
4. Git-native delta indexing. A re-index walks the diff of the HEAD tree. Unchanged blobs are not read, parsed or embedded again. A one-file commit re-indexes in less than one second.
5. An independent semantic plane. The vector index is derived from the store and the shards. You can change the embedding model or rebuild the plane without touching the lexical index.

Data layout:

<data-dir>/
  shards/*.cidx          immutable index shards (mmap'd)
  cas/v2/<hh>/<rest>     content-addressed extracted artifacts (zstd)
  embcas/<model>/        content-addressed embeddings, one pack per model
  vec/<model>.*.civec    int8 vector segments with a binary prescan
  bm25/*.cibm25          chunk-level BM25 sidecar (mmap'd)
  sem/*.rimodel          the built-in semantic model (mmap'd)
  repos/<name>.json      per-repository state
  sessions/              rendered session transcripts for recall (30-day window)
  runs/<repo>/*.log      command output kept by `indexio run` (30-day window)
  usage/<day>.jsonl      the MCP usage log

Measured performance

Storage and start-up, measured on the author's machine on a 44-repository, 10,000-file data directory (docs/SPEC-P10.md):

The same lookups through the shell and through the index (bench/ab_speed.py, this repository, a 1,300-file TypeScript application gives the same picture). Wall-clock, medians of 10, the index side includes the MCP transport:

Each Bash tool call also pays about 15 ms for the shell and about 30 ms for the two PreToolUse hooks before its command runs. An MCP call pays neither. On real traffic (5,355 calls in 7 days) the median is 0 ms for read_span, 12 ms for code_search and 29 ms for code_grep; the 90th percentile stays under 130 ms.

Duplication, measured on a sandbox with 2 cores and 4 GB of RAM:

Lexical latency on the same sandbox: rare identifier 21 ms, common term 81 ms, regex 254 ms. Delta re-index of a one-file commit: 792 ms.

Semantic quality on 20 concept queries (bench/known_answers20.json, bench/eval_modes.py):

Measured and rejected: CombMNZ fusion scored below RRF. An offline overlap reranker scored below hybrid alone. Thesaurus query expansion scored below plain semantic search. An IVF prescan gave no speed-up. These stay off by default.

Limits

• No type-resolved cross-references. Call edges are name-based. Overloaded names such as new, get and run produce noise. Filter by caller and path.
• Untracked files in impact --diff. git diff does not include them. Stage them, or pass a patch.
• The built-in model is not neural. It is useful and cheap. For neural quality, set INDEXIO_EMBED_BASE.
• MCP has no authentication. It runs as the local user over stdio. Do not expose it to a network without a gateway.
• No web UI and no distributed query. One binary, one data directory.

Development and releases

cargo test --workspace                  # every crate, 325 tests
cargo clippy --workspace --all-targets
tools/build-release.sh                  # release build; remaps local paths out of the binary

Crates: indexio-types (shared types, posting codec), indexio-core (n-grams, verification, query literals), indexio-index (shards, merge, tombstones), indexio-symbols (tree-sitter symbols, calls and chunks for 6 languages), indexio-ingest (git delta, content store, sources), indexio-embed (embedders, embedding store, vector index, pipeline), indexio-query (planner, ranking, fusion, impact), indexio (CLI, HTTP, MCP, hooks). The design notes are in docs/; docs/DEVELOPMENT.md is the operator manual.

CI (.github/workflows/ci.yml) runs on each push and pull request. It checks that the manifests parse, the scripts compile and the workflows are valid. It is killed after 90 seconds. The build and the test suite run locally; they do not fit that budget.

Releases (.github/workflows/release.yml) come from main:

1. Set version in Cargo.toml ([workspace.package]).
2. Merge to main. In less than 90 seconds the workflow creates the tag v<version> and a GitHub release with generated notes. A merge without a version change does nothing.
3. The same workflow then builds the binaries for Linux (x86_64, aarch64), macOS (Apple silicon, Intel) and Windows (x86_64), attaches each archive with a .sha256 and a pip wheel to the release, publishes the container image to ghcr.io, publishes the npm package when the NPM_TOKEN secret exists, and publishes the indexio-cli wheels to PyPI when the PYPI_API_TOKEN secret exists. These jobs compile Rust and take some minutes.

tools/release-assets.sh builds and attaches one asset from a maintainer machine, for a platform the workflow does not cover.

License

Apache License 2.0. See LICENSE and NOTICE.