@cerefox/memory 0.4.3 → 0.5.1

package/docs/guides/connect-agents.md

@@ -0,0 +1,1428 @@
+# Connecting AI Agents to Cerefox
+
+Cerefox exposes your knowledge base through two access paths. Choose the one that fits your
+client; you can also run both in parallel.
+
+> **OpenAI API key — known glitch (all paths):** The simplest setup is an **unrestricted**
+> OpenAI API key — it just works. If you prefer a restricted key and hit a
+> `Missing scopes: model.request` or 401 error despite the key looking correct in the
+> dashboard, this is a [known OpenAI UI bug](https://community.openai.com/t/missing-scopes-model-request-on-restricted-api-key/1371602):
+> narrowing sub-scopes after setting the top-level **Model Capabilities → Write** permission
+> corrupts the internal permission state silently. The fix is either to switch to an
+> unrestricted key, or to open the key in the
+> [OpenAI dashboard](https://platform.openai.com/api-keys), save it without any changes, and
+> retry — this resets the internal state immediately.
+>
+> This applies to all paths (A-Local, A-Remote, Path B) — any path that calls the OpenAI
+> embedding API can be affected. If you're on Fireworks AI instead, see
+> `docs/guides/configuration.md` → "Changing the embedding model".
+
+---
+
+## Access paths at a glance
+
+Three top-level paths plus a few special cases:
+
+- **Path A** — MCP server (local subprocess or remote Edge Function). Best for purpose-built agent clients like Claude Desktop, Cursor, and Claude Code's MCP integration.
+- **Path B** — direct Edge Function HTTP. Best for ChatGPT Custom GPTs and any HTTP caller (curl, scripts).
+- **Path C** — local shell CLI invoked by a coding agent's Bash tool. Best for Claude Code, Codex CLI, opencode, OpenClaw, Hermes, and similar local-agent CLIs **when the user prefers not to configure MCP** but still wants the agent to read and write Cerefox.
+
+| Client | Path | Search | Requirements / caveats |
+|--------|------|--------|-----------------------|
+| Claude Desktop (remote) | Path A-Remote — `cerefox-mcp` Edge Function | Hybrid | Node.js for `npx supergateway` or `npx mcp-remote`; no Python needed |
+| Claude Code (remote) | Path A-Remote — `cerefox-mcp` Edge Function | Hybrid | URL + anon key only; no local install |
+| Cursor (remote) | Path A-Remote — `cerefox-mcp` Edge Function | Hybrid | URL + anon key only; no local install |
+| OpenAI Codex CLI (remote) | Path A-Remote — `cerefox-mcp` Edge Function | Hybrid | URL + anon key env var; TOML config |
+| ChatGPT (chatgpt.com or desktop) | Path B — Custom GPT → Edge Functions | Hybrid | ChatGPT Plus required |
+| Claude Desktop (local) | Path A-Local — `@cerefox/memory` via `npx` (recommended) or `cerefox mcp` (Python fallback) | Hybrid | Local alternative; Node.js (npm path) or Python + uv + local clone (legacy path); zero Edge Function invocations |
+| Claude Code (local) | Path A-Local — `@cerefox/memory` via `npx` or `cerefox mcp` | Hybrid | Local alternative; zero Edge Function invocations |
+| Cursor (local) | Path A-Local — `@cerefox/memory` via `npx` or `cerefox mcp` | Hybrid | Local alternative; zero Edge Function invocations |
+| Cloud Claude (claude.ai web) | Remote Supabase MCP | FTS only | No install; search quality limited |
+| Gemini CLI (remote) | Path A-Remote — `cerefox-mcp` Edge Function | Hybrid | URL + anon key only; no local install |
+| Local coding agents (Claude Code, Codex CLI, opencode, OpenClaw, Hermes, …) | Path C — Shell CLI (Bash tool) | Hybrid | Local clone + `uv`; agent runs `uv run cerefox …` as a shell command. Useful when MCP setup is friction. |
+| curl / scripts | Path B — Edge Functions directly | Hybrid | Direct HTTP; no client needed |
+| Custom Python agents | Python SDK directly | Hybrid | Local Python required |
+
+> **"Hybrid"** = FTS + semantic, document-level (complete reconstructed notes, not isolated chunks).
+> **"FTS only"** = keyword search only; no semantic/vector search.
+
+> **Cloud hybrid for all clients (future)**: deploying the MCP server to Cloud Run would give
+> cloud clients (claude.ai, chatgpt.com) full hybrid search. Tracked in `docs/TODO.md`.
+
+> **Perplexity** supports stdio-only MCP on macOS Desktop (via Helper App). Remote MCP is
+> "coming soon." Perplexity's CTO has signalled a strategic shift away from MCP (March 2026),
+> so API-based integration may be the long-term path. Not a priority.
+>
+> **Gemini web** (gemini.google.com) does not support custom MCP servers. No integration path.
+
+> **Quick start with templates:** Copy-pasteable `.mcp.json` templates for each client are
+> available in [`examples/mcp-configs/`](../examples/mcp-configs/). Pick the one for your
+> client, replace the placeholders, and you're connected.
+
+---
+
+## Prerequisites
+
+**For all paths:**
+- Supabase project set up and schema deployed (see `setup-supabase.md`)
+- Some content ingested (`cerefox ingest my-notes.md`)
+
+**For Path A-Local only:**
+- **Recommended (v0.4.0+):** [Node.js ≥20](https://nodejs.org) (for `npx --package=@cerefox/memory cerefox mcp`)
+  + `.env` file in the working directory the client launches the server from (see "env block"
+  in the per-client configs below if your client can't see the file)
+- **Alternative:** [`uv`](https://docs.astral.sh/uv/getting-started/installation/) installed on your machine + Cerefox repository cloned locally (e.g. `/Users/yourname/src/cerefox`)
+  + `.env` in the checkout
+- Either way, `.env` must define `CEREFOX_SUPABASE_URL`, `CEREFOX_SUPABASE_KEY`, and your
+  embedding API key (`OPENAI_API_KEY`)
+
+> **Important — which anon key to use (2026):** Path A-Remote and Path B both require an
+> "anon key" as a Bearer token. As of 2026, you **must** use the **legacy anon JWT**
+> (`eyJ…`) — the new `sb_publishable_…` key is rejected by the Supabase Edge Function
+> gateway with `UNAUTHORIZED_INVALID_JWT_FORMAT`. Find the legacy key in **Project
+> Settings → API Keys → Legacy → anon**. This is a Supabase platform constraint;
+> see [`setup-supabase.md` → Supabase API keys (2026)](setup-supabase.md#supabase-api-keys-2026)
+> for the full story.
+
+**For Path A-Remote (remote MCP Edge Function) — recommended:**
+- `cerefox-mcp` Edge Function deployed (`npx supabase functions deploy cerefox-mcp`)
+- Your **legacy anon JWT** (see callout above): Supabase Dashboard → Project Settings → API Keys → Legacy → anon
+- For Claude Desktop: [Node.js](https://nodejs.org) installed (for `npx supergateway` or `npx mcp-remote`)
+- For Claude Code: [Node.js](https://nodejs.org) for `npx mcp-remote` (recommended), or no extra deps for native HTTP
+
+**For Path B (Edge Functions / GPT Actions) only:**
+- Supabase Edge Functions deployed: `cerefox-search`, `cerefox-ingest`, `cerefox-metadata`,
+  `cerefox-get-document`, `cerefox-list-versions`, `cerefox-get-audit-log`,
+  `cerefox-metadata-search`, `cerefox-list-projects` --
+  see `setup-supabase.md` for the deploy procedure (`npx supabase functions deploy`)
+- Your **legacy anon JWT** (see callout above): Supabase Dashboard → Project Settings → API Keys → Legacy → anon
+- Your **project ref**: visible in the Supabase Dashboard URL
+  (`app.supabase.com/project/<project-ref>`)
+
+**For cloud Claude.ai only:**
+- A **Personal Access Token** (PAT): create at `https://supabase.com/dashboard/account/tokens`
+
+---
+
+## Path A-Local — Local MCP server
+
+### What it is
+
+The local Cerefox MCP server runs on your machine and exposes the same 10 tools as the remote
+Edge Function, communicating with clients over stdio.
+
+As of **v0.4.0** the local server ships as an npm package — **[`@cerefox/memory`](https://www.npmjs.com/package/@cerefox/memory)** — built with the official `@modelcontextprotocol/sdk`.
+The bin entry is `cerefox` (run as `cerefox mcp`). The recommended client config is `npx -y --package=@cerefox/memory cerefox mcp`.
+
+The legacy `uv run cerefox mcp` invocation **still works** and is preserved as a soft
+wrapper: it tries `npx --no-install @cerefox/memory cerefox mcp` first and falls back to the
+Python MCP server if npm is unavailable or `@cerefox/memory` isn't installed. New users
+should prefer the npm-native config; existing users don't have to change anything.
+
+- Embeddings are computed locally using your `.env` key (no extra credentials)
+- Works offline except for the OpenAI embedding API call per query
+- One setup, all compatible local clients (Claude Desktop, Cursor, Claude Code, Codex CLI, …)
+
+See [`docs/guides/migration-v0.4.md`](migration-v0.4.md) for before/after config snippets
+per client.
+
+> **Why not `mcp-server-fetch`?** The generic fetch MCP only supports GET requests and cannot
+> make authenticated POST calls to the Edge Functions. The built-in local server is
+> the correct solution.
+
+### Path A MCP tools
+
+Once configured, every Path A client has these tools:
+
+| Tool | Description |
+|------|-------------|
+| `cerefox_search` | Hybrid (FTS + semantic) document-level search. Filter by `project_name` or `metadata_filter`. |
+| `cerefox_ingest` | Save a note or document to the knowledge base. Pass `document_id` to update by ID (deterministic); or `update_if_exists: true` to update by title match. Accepts optional `author` and `project_name`. |
+| `cerefox_list_metadata_keys` | List all metadata keys in use across documents |
+| `cerefox_get_document` | Retrieve the full content of a document (current or archived version) |
+| `cerefox_list_versions` | List all archived versions of a document |
+| `cerefox_get_audit_log` | Query audit log entries with filters (document, author, operation, time range) |
+| `cerefox_list_projects` | List all projects with names and IDs. Use for discovering available projects. |
+| `cerefox_metadata_search` | Find documents by metadata key-value criteria without a text search term. Supports project, date, and content filters. |
+| `cerefox_set_document_projects` | Set a document's project memberships to exactly the given list (destructive replace; metadata-only, no content change). Use `cerefox_ingest` with singular `project_name` for non-destructive "add". |
+| `cerefox_get_help` | Retrieve Cerefox conventions (the same content as `AGENT_QUICK_REFERENCE.md`) over MCP. Optional `topic` parameter does a case-insensitive H2 substring match. Call this whenever you are uncertain. |
+
+> All 10 tools are available on both Path A (local and remote MCP) and Path B (GPT Actions
+> via dedicated Edge Functions, except `cerefox_get_help` which is MCP-only). MCP tools use
+> `project_name` (human-readable); primitive Edge Functions (Path B) use `project_id` (UUID).
+
+### Path A system prompt
+
+Set this as Custom Instructions / System Prompt in your client:
+
+```
+You have access to a personal knowledge base via Cerefox MCP tools.
+When answering questions, always call cerefox_search first with a relevant query.
+Cite doc_title for every claim drawn from the knowledge base.
+Use cerefox_ingest to save anything the user asks you to remember.
+Always set your requestor/author parameter to identify yourself.
+For the full tool reference, search Cerefox for "How AI Agents Use Cerefox".
+```
+
+> **Agent reference docs**: `AGENT_GUIDE.md` (comprehensive) and `AGENT_QUICK_REFERENCE.md` (quick
+> reference) in the repo root contain the full tool reference for AI agents. These are also
+> ingested into the Cerefox KB via `sync_docs.py`, so agents can find them by searching.
+
+### Path A verification prompts
+
+After setup, ask your client:
+
+> "What tools do you have available?"
+> Expected: 10 tools listed (`cerefox_search`, `cerefox_ingest`, `cerefox_get_document`,
+> `cerefox_list_versions`, `cerefox_list_projects`, `cerefox_list_metadata_keys`,
+> `cerefox_metadata_search`, `cerefox_set_document_projects`, `cerefox_get_audit_log`,
+> `cerefox_get_help`).
+
+> "Use cerefox_search with query='second brain' and match_count=3. What did you find?"
+
+> "Save a note titled 'Test Note' with content '# Test\nThis is a test.' using cerefox_ingest."
+
+> "Call cerefox_get_help with no topic. What sections are listed?"
+
+---
+
+### Claude Desktop
+
+**Config file location:**
+- macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
+- Windows: `%APPDATA%\Claude\claude_desktop_config.json`
+
+**Recommended — npm (`@cerefox/memory`, v0.4.0+):**
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "npx",
+      "args": ["-y", "--package=@cerefox/memory", "cerefox", "mcp"],
+      "env": {
+        "CEREFOX_SUPABASE_URL": "https://<your-project-ref>.supabase.co",
+        "CEREFOX_SUPABASE_KEY": "<your-service-role-or-sb_secret-key>",
+        "OPENAI_API_KEY": "sk-..."
+      }
+    }
+  }
+}
+```
+
+The `env` block is only needed if you don't already have a `.env` file in a directory the
+server can find — the server resolves `.env` from the current working directory.
+
+**Alternative — local checkout (Python or pre-v0.4 setups):**
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "uv",
+      "args": ["--directory", "/path/to/cerefox", "run", "cerefox", "mcp"]
+    }
+  }
+}
+```
+
+Replace `/path/to/cerefox` with the absolute path to your Cerefox checkout
+(e.g. `/Users/yourname/src/cerefox` on macOS, `C:\Users\yourname\src\cerefox` on Windows).
+This invocation soft-wraps `npx --package=@cerefox/memory cerefox mcp` when available; otherwise the
+legacy Python MCP server takes over.
+
+**Important:**
+- Merge the `mcpServers` block into any existing `claude_desktop_config.json` — do not wrap it
+  in an extra `{}` or replace the whole file.
+- Restart Claude Desktop fully (Cmd+Q on macOS, not just close the window) after saving.
+
+---
+
+### ChatGPT Desktop
+
+> **ChatGPT Desktop does not support local stdio MCP servers.**
+> OpenAI's MCP implementation for ChatGPT only supports remote servers via SSE or
+> streaming HTTP — not local subprocess (stdio) servers like `cerefox mcp`.
+> The "dev mode" MCP connector visible in the app also requires a public URL.
+>
+> **Use Path B (Custom GPT + Edge Functions) for all ChatGPT access** — both the web
+> app and the desktop app. The Custom GPT approach is fully validated and works well.
+
+---
+
+### Cursor
+
+1. Open **Cursor Settings** (`Cmd+,`) → **Tools & Integrations** → **MCP** → **Add new global MCP server**
+2. Paste either of the following into the MCP config JSON:
+
+**Recommended — npm:**
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "npx",
+      "args": ["-y", "--package=@cerefox/memory", "cerefox", "mcp"],
+      "env": {
+        "CEREFOX_SUPABASE_URL": "https://<your-project-ref>.supabase.co",
+        "CEREFOX_SUPABASE_KEY": "<your-service-role-or-sb_secret-key>",
+        "OPENAI_API_KEY": "sk-..."
+      }
+    }
+  }
+}
+```
+
+**Alternative — local checkout:**
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "uv",
+      "args": ["--directory", "/path/to/cerefox", "run", "cerefox", "mcp"]
+    }
+  }
+}
+```
+
+3. Save and restart Cursor.
+
+Alternatively, add a `.cursor/mcp.json` file in your project root with the same content for
+project-scoped access (committed to git, shared with your team).
+
+---
+
+### Claude Code
+
+Claude Code (the CLI tool and the **Code** tab inside Claude Desktop) uses its own MCP config —
+separate from `claude_desktop_config.json`. Changes made in one do not affect the other.
+
+**Option 1: CLI command — npm (recommended)**
+
+```bash
+claude mcp add --scope user cerefox \
+  npx -- -y --package=@cerefox/memory cerefox mcp
+```
+
+- `--scope user` makes the server available in every project (stored in `~/.claude/mcp.json`).
+- Use `--scope project` instead to limit it to the current directory (stored in `.mcp.json`).
+
+If you don't already have `.env` resolvable from your shell's CWD, add the credentials inline
+by editing the resulting JSON config to add an `env` block (see the Claude Desktop example
+above).
+
+Verify:
+```bash
+claude mcp list
+```
+
+**Option 2: CLI command — local checkout (uv)**
+
+```bash
+claude mcp add --scope user cerefox \
+  uv -- --directory /path/to/cerefox run cerefox mcp
+```
+
+This soft-wraps `npx --package=@cerefox/memory cerefox mcp` when available; otherwise falls back to
+the legacy Python MCP server.
+
+**Option 3: `.mcp.json` in project root (project-scoped, committable)**
+
+Create `.mcp.json` in the root of the repo you work in:
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "npx",
+      "args": ["-y", "--package=@cerefox/memory", "cerefox", "mcp"]
+    }
+  }
+}
+```
+
+**Code tab inside Claude Desktop:**
+The **Code** tab in Claude Desktop uses the same config as the Claude Code CLI, not
+`claude_desktop_config.json`. Run the `claude mcp add` command above — the Code tab will
+pick it up automatically.
+
+---
+
+## Path A-Remote — Remote MCP Edge Function (`cerefox-mcp`)
+
+### What it is
+
+`cerefox-mcp` is a Supabase Edge Function that speaks the MCP Streamable HTTP protocol
+(spec 2025-03-26). It calls Postgres RPCs directly via per-tool handlers -- no delegation
+to primitive Edge Functions. This means each MCP tool call costs a single Edge Function
+invocation.
+
+A single HTTPS URL gives any remote-capable MCP client all 10 tools with full hybrid
+search -- no Python, no `uv`, no local repository clone needed.
+
+**URL format:**
+```
+https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp
+```
+
+**When to choose Path A-Remote vs Path A-Local:**
+
+| Scenario | Prefer |
+|----------|--------|
+| Default / new setup | Path A-Remote -- no Python, no local clone, one URL works everywhere |
+| Multiple machines / cloud dev environments | Path A-Remote |
+| Minimise Supabase Edge Function usage (free tier limits) | Path A-Local -- zero Edge Function invocations |
+| Offline use or development on the cerefox codebase | Path A-Local -- no network dependency |
+| Lowest latency (same machine, no HTTPS round-trip) | Path A-Local -- slightly faster |
+
+**Deploy the Edge Function** (once, after cloning the repo):
+```bash
+npx supabase functions deploy cerefox-mcp
+```
+
+---
+
+### Path A-Remote: Claude Code
+
+> **Recommended: use `mcp-remote` stdio bridge.** While the SSE idle polling issue has been
+> fixed server-side (v0.1.12 -- the server returns 405 for GET per the MCP spec), `mcp-remote`
+> is still recommended because it cleanly bypasses Supabase's GoTrace OAuth discovery conflict
+> via `--header`. See [issue #17](https://github.com/fstamatelopoulos/cerefox/issues/17) for
+> the full investigation.
+
+**Option 1 — `mcp-remote` (recommended):**
+
+Add to your project's `.mcp.json` (or copy
+[`examples/mcp-configs/claude-code-remote.json`](../examples/mcp-configs/claude-code-remote.json)):
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "npx",
+      "args": [
+        "mcp-remote",
+        "https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp",
+        "--header",
+        "Authorization: Bearer <your-anon-key>"
+      ]
+    }
+  }
+}
+```
+
+**Option 2 — native HTTP:**
+
+Claude Code also supports Streamable HTTP natively. This works and no longer has idle polling
+overhead (fixed in v0.1.12). However, `mcp-remote` is still preferred for the OAuth bypass.
+
+```bash
+claude mcp add --transport http cerefox \
+  https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp \
+  --header "Authorization: Bearer <your-anon-key>"
+```
+
+Verify:
+```bash
+claude mcp list
+```
+
+For a user-scoped server (available in all projects), add `--scope user`:
+```bash
+claude mcp add --transport http --scope user cerefox \
+  https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp \
+  --header "Authorization: Bearer <your-anon-key>"
+```
+
+---
+
+### Path A-Remote: Cursor
+
+Cursor supports remote MCP servers natively via `url` + `headers` in `mcp.json`.
+
+1. Open **Cursor Settings** (`Cmd+,`) → **Tools & Integrations** → **MCP** → **Add new global MCP server**
+2. Paste this config (replace the placeholders):
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "url": "https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp",
+      "headers": {
+        "Authorization": "Bearer <your-anon-key>"
+      }
+    }
+  }
+}
+```
+
+3. Save and restart Cursor.
+
+Alternatively, add `.cursor/mcp.json` in your project root with the same content for
+project-scoped access.
+
+---
+
+### Path A-Remote: Claude Desktop
+
+Claude Desktop does not support remote MCP servers natively -- it requires a local subprocess
+(`command` field). Use [`supergateway`](https://www.npmjs.com/package/supergateway) or
+[`mcp-remote`](https://www.npmjs.com/package/mcp-remote) as a stdio-to-HTTP bridge.
+
+> **`supergateway` vs `mcp-remote` for Claude Desktop:** `mcp-remote --header` works for
+> Claude Code (tested). For Claude Desktop, `supergateway` is the tested and confirmed option.
+> `mcp-remote` may also work for Claude Desktop now that the 405 SSE fix is in place, but
+> this has not been verified. If you try it, use the same config as Claude Code.
+
+**Requirements:** [Node.js](https://nodejs.org) installed (for `npx`).
+
+**Config file location:**
+- macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
+- Windows: `%APPDATA%\Claude\claude_desktop_config.json`
+
+Add (or merge into) the file:
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "command": "npx",
+      "args": [
+        "-y", "supergateway",
+        "--streamableHttp", "https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp",
+        "--oauth2Bearer", "<your-anon-key>"
+      ]
+    }
+  }
+}
+```
+
+Replace `<your-project-ref>` and `<your-anon-key>` with your actual values.
+
+**Important:**
+- Restart Claude Desktop fully (Cmd+Q on macOS) after saving the config.
+- `-y` tells npx to auto-install `supergateway` without prompting.
+- No Python, no local repo clone, no `.env` file needed — just the URL and anon key.
+
+---
+
+### Path A-Remote: OpenAI Codex CLI
+
+[Codex](https://github.com/openai/codex) supports remote MCP servers natively via Streamable
+HTTP. Configuration uses TOML (not JSON like most other MCP clients).
+
+**Step 1 — Set the anon key as an environment variable:**
+
+Codex references Bearer tokens by environment variable name, not by value. Add to your
+`~/.zshrc` (or `~/.bashrc`):
+
+```bash
+export CEREFOX_ANON_KEY="<your-anon-key>"
+```
+
+Then reload: `source ~/.zshrc`
+
+**Step 2 — Add the server to `~/.codex/config.toml`:**
+
+```toml
+[mcp_servers.cerefox]
+url = "https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp"
+bearer_token_env_var = "CEREFOX_ANON_KEY"
+```
+
+Replace `<your-project-ref>` with your Supabase project ref.
+
+**Step 3 — Verify:**
+
+Launch Codex and use the `/mcp` slash command to confirm the `cerefox` server is connected
+and all 10 tools are listed.
+
+**Notes:**
+- `bearer_token_env_var` is the **name** of the env var (e.g. `"CEREFOX_ANON_KEY"`), not the
+  token itself. Codex reads the value at runtime.
+- No Python, no local repo clone needed — just the URL and anon key.
+- No idle SSE polling cost — the 405 GET fix in `cerefox-mcp` prevents it.
+
+---
+
+### Path A-Remote: Gemini CLI
+
+[Gemini CLI](https://github.com/google-gemini/gemini-cli) supports Streamable HTTP with static
+Bearer token headers natively — no bridge needed. Architecturally identical to Claude Code and
+Cursor.
+
+**Config file location:**
+- Global: `~/.gemini/settings.json`
+- Project: `.gemini/settings.json` in the project root
+
+Add (or merge into) the file:
+
+```json
+{
+  "mcpServers": {
+    "cerefox": {
+      "httpUrl": "https://<your-project-ref>.supabase.co/functions/v1/cerefox-mcp",
+      "headers": {
+        "Authorization": "Bearer <your-anon-key>"
+      }
+    }
+  }
+}
+```
+
+Replace `<your-project-ref>` and `<your-anon-key>` with your actual values.
+
+**Verify:**
+
+Launch `gemini` and use `/mcp` to confirm tools are listed, or ask:
+> "What tools do you have available?"
+
+**Notes:**
+- Use `httpUrl` (not `url`) for Streamable HTTP transport.
+- Static headers bypass OAuth discovery entirely — no GoTrue conflict.
+- No Python, no local repo clone needed.
+- Status: **untested** — expected to work based on architecture match with Claude Code/Cursor.
+
+---
+
+## Path B — Supabase Edge Functions (HTTP)
+
+### What they are
+
+TypeScript functions deployed to Supabase, callable over HTTPS from anywhere — no local install,
+no MCP client needed. Embeddings are computed server-side using the `OPENAI_API_KEY` secret
+stored in Supabase.
+
+- Works from cloud agents (ChatGPT GPT Actions, scripts, CI pipelines)
+- No user machine required; Supabase handles all infrastructure
+- Constraint: embedding model is hardcoded in TypeScript — requires redeployment when changed
+  (see `docs/guides/configuration.md` → "Changing the embedding model")
+
+### Path B authentication
+
+All Edge Function calls require:
+
+```
+Authorization: Bearer <your-anon-key>
+Content-Type: application/json
+```
+
+Find your anon key: **Supabase Dashboard → Project Settings → API Keys → Legacy → anon** (use the legacy JWT, not the new `sb_publishable_…` — see the API keys callout in the Prerequisites section).
+
+### Path B system prompt
+
+For ChatGPT Custom GPT:
+```
+You have access to a personal knowledge base via the searchKnowledgeBase action.
+When the user asks a question, always search the knowledge base first using a
+relevant query. Present results by document title, citing the source for every claim.
+Use ingestNote to save any new information the user asks you to remember.
+```
+
+### Path B verification
+
+```bash
+curl -s -X POST \
+  "https://<your-project-ref>.supabase.co/functions/v1/cerefox-search" \
+  -H "Authorization: Bearer <your-anon-key>" \
+  -H "Content-Type: application/json" \
+  -d '{"query": "second brain", "match_count": 3}'
+```
+
+Expected: JSON response with `results` array containing documents.
+
+---
+
+### ChatGPT Custom GPT (cloud — chatgpt.com)
+
+A Custom GPT with Actions pointing at the Edge Functions gives ChatGPT full hybrid search from
+any browser — no local install, no MCP client, works free with ChatGPT Plus.
+
+**Step 1 — Create the Custom GPT**
+
+1. Go to **chatgpt.com → Explore GPTs → Create**
+2. Name it (e.g. "Cerefox Assistant")
+3. Paste the system prompt from "Path B system prompt" above into the **Instructions** field
+4. Click **Create new action**
+
+**Step 2 — Paste the OpenAPI schema**
+
+In the action editor, paste this schema (replace `<your-project-ref>`):
+
+```yaml
+openapi: 3.1.0
+info:
+  title: Cerefox Knowledge Base
+  version: 1.7.0
+servers:
+  - url: https://<your-project-ref>.supabase.co/functions/v1
+paths:
+  /cerefox-search:
+    post:
+      operationId: searchKnowledgeBase
+      summary: Search the knowledge base (hybrid FTS + semantic, document-level)
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              required: [query]
+              properties:
+                query:
+                  type: string
+                match_count:
+                  type: integer
+                  default: 5
+                project_name:
+                  type: string
+                mode:
+                  type: string
+                  default: docs
+                metadata_filter:
+                  type: object
+                  additionalProperties:
+                    type: string
+                  description: >
+                    Optional JSONB containment filter. Only documents whose metadata
+                    contains ALL specified key-value pairs are returned.
+                    Example: {"type": "decision", "status": "active"}.
+                    Call listMetadataKeys to discover available keys and their values.
+                    Omit or set to null to search all documents.
+                requestor:
+                  type: string
+                  description: >
+                    Name of the agent making this request (e.g., "ChatGPT").
+                    Recorded in the usage log for attribution. Optional.
+      responses:
+        '200':
+          description: >
+            { results, query, mode, match_count, project_name, metadata_filter, truncated, response_bytes }.
+            Each item in results (docs mode) contains: document_id, doc_title, full_content,
+            chunk_count, total_chars, best_score, is_partial.
+            is_partial is true when the document exceeded the small-to-big threshold — in that
+            case full_content contains matched chunks plus their neighbours rather than the
+            complete document, and total_chars still reflects the full document size.
+  /cerefox-ingest:
+    post:
+      operationId: ingestNote
+      summary: >
+        Save a note to the knowledge base. When update_if_exists is true and the
+        document already exists, the previous version is archived automatically —
+        you can retrieve it later with getDocument.
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              required: [title, content]
+              properties:
+                title:
+                  type: string
+                content:
+                  type: string
+                document_id:
+                  type: string
+                  description: >
+                    UUID of an existing document to update. When provided, updates
+                    that document directly regardless of update_if_exists. Returns
+                    an error if the document does not exist. Workflow: search for
+                    the document, note the document_id, pass it here.
+                project_name:
+                  type: string
+                source:
+                  type: string
+                  default: agent
+                metadata:
+                  type: object
+                update_if_exists:
+                  type: boolean
+                  default: false
+                  description: >
+                    When true, update an existing document with the same title
+                    instead of creating a new one. The previous content is archived
+                    as a version. If content is unchanged, the document is skipped
+                    (no re-indexing). Ignored when document_id is provided.
+                author:
+                  type: string
+                  description: >
+                    Name of the agent or tool performing the ingestion (e.g.,
+                    "ChatGPT", "Claude Code"). Recorded in the audit log for
+                    attribution. Defaults to "agent" if not provided.
+                author_type:
+                  type: string
+                  enum: [user, agent]
+                  default: agent
+                  description: >
+                    Whether this write is from a human user or an AI agent.
+                    Controls review_status auto-transition: agent writes set
+                    the document to pending_review, user writes set it to approved.
+      responses:
+        '200':
+          description: Ingest result
+  /cerefox-metadata:
+    post:
+      operationId: listMetadataKeys
+      summary: List all metadata keys in use across documents with counts and example values
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: Array of metadata keys with doc_count and example_values
+  /cerefox-get-document:
+    post:
+      operationId: getDocument
+      summary: >
+        Retrieve the full reconstructed content of a document (current version or a specific
+        archived version). Use listVersions first to discover available version UUIDs.
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              required: [document_id]
+              properties:
+                document_id:
+                  type: string
+                  description: UUID of the document to retrieve
+                version_id:
+                  type: string
+                  description: >
+                    UUID of a specific archived version to retrieve. Omit (or pass null)
+                    for the current version. Version UUIDs are returned by listVersions.
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: >
+            Document content and metadata:
+            { document_id, doc_title, full_content, chunk_count, total_chars,
+              is_archived, version_id }
+        '404':
+          description: Document not found
+  /cerefox-list-versions:
+    post:
+      operationId: listVersions
+      summary: >
+        List all archived versions of a document, newest first. Returns version UUIDs
+        to pass to getDocument for historical content retrieval.
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              required: [document_id]
+              properties:
+                document_id:
+                  type: string
+                  description: UUID of the document whose version history to list
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: >
+            Array of version objects (empty array if no versions exist):
+            [{ version_id, version_number, source, chunk_count, total_chars, archived, created_at }]
+  /cerefox-get-audit-log:
+    post:
+      operationId: getAuditLog
+      summary: >
+        Query audit log entries with optional filters. Returns entries with document
+        titles, author attribution, operation types, size changes, and descriptions.
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                document_id:
+                  type: string
+                  description: Filter by document UUID (optional)
+                author:
+                  type: string
+                  description: Filter by author name (optional)
+                operation:
+                  type: string
+                  description: >
+                    Filter by operation type: create, update-content, update-metadata,
+                    delete, status-change, archive, unarchive (optional)
+                since:
+                  type: string
+                  description: ISO timestamp lower bound for temporal queries (optional)
+                limit:
+                  type: integer
+                  default: 50
+                  description: Max entries to return (max 200)
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: >
+            Array of audit log entries:
+            [{ id, document_id, doc_title, version_id, operation, author, author_type,
+               size_before, size_after, description, created_at }]
+  /cerefox-list-projects:
+    post:
+      operationId: listProjects
+      summary: List all projects with their names, IDs, and descriptions
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: >
+            Array of projects: [{ id, name, description }]
+  /cerefox-metadata-search:
+    post:
+      operationId: metadataSearch
+      summary: >
+        Find documents by metadata key-value criteria without a text search term.
+        Use to discover documents tagged with specific attributes or browse by taxonomy.
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              required: [metadata_filter]
+              properties:
+                metadata_filter:
+                  type: object
+                  additionalProperties:
+                    type: string
+                  description: >
+                    Key-value pairs; ALL must match (AND semantics).
+                    Example: {"type": "decision", "status": "active"}.
+                project_id:
+                  type: string
+                  description: Filter by project UUID (optional)
+                updated_since:
+                  type: string
+                  description: ISO-8601 timestamp; only docs updated on/after (optional)
+                created_since:
+                  type: string
+                  description: ISO-8601 timestamp; only docs created on/after (optional)
+                limit:
+                  type: integer
+                  default: 10
+                include_content:
+                  type: boolean
+                  default: false
+                  description: Include full document text in results
+                requestor:
+                  type: string
+                  description: Name of the agent making this request. Optional.
+      responses:
+        '200':
+          description: >
+            Array of matching documents:
+            [{ document_id, title, doc_metadata, review_status, source, created_at,
+               updated_at, total_chars, chunk_count, project_ids, project_names,
+               version_count, content }]
+```
+
+**Step 3 — Configure authentication**
+
+In the action's **Authentication** settings:
+- Type: **API Key**
+- Auth type: **Bearer**
+- API key: your Supabase **anon key**
+
+> **Important:** ChatGPT may reset the API key when you update the action schema.
+> If you get a 403 error after changing the schema, re-enter the anon key in the
+> authentication settings — the functions themselves are fine.
+
+**Step 4 — Save and test**
+
+Save the GPT. In a new chat, ask:
+> "Search my knowledge base for 'second brain'."
+
+> **Cost**: GPT Actions are free with ChatGPT Plus. Each search call uses a small amount of
+> OpenAI API credits for embedding the query. See `docs/guides/operational-cost.md`.
+
+---
+
+### curl / scripts
+
+Direct HTTP access — useful for shell scripts, CI pipelines, or one-off queries.
+
+**Search:**
+```bash
+curl -s -X POST \
+  "https://<your-project-ref>.supabase.co/functions/v1/cerefox-search" \
+  -H "Authorization: Bearer <your-anon-key>" \
+  -H "Content-Type: application/json" \
+  -d '{"query": "knowledge management", "match_count": 5}'
+```
+
+**Ingest:**
+```bash
+curl -s -X POST \
+  "https://<your-project-ref>.supabase.co/functions/v1/cerefox-ingest" \
+  -H "Authorization: Bearer <your-anon-key>" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "title": "Meeting Notes 2026-03-11",
+    "content": "# Meeting Notes\n\n## Q1 Roadmap\n\nWe agreed to prioritize...",
+    "project_name": "Work",
+    "source": "agent"
+  }'
+```
+
+If the same content was already ingested (SHA-256 hash match), returns `"skipped": true`.
+
+**Edge Function parameters — `cerefox-search`:**
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `query` | string | required | Natural-language search query |
+| `project_name` | string | optional | Filter by project name (case-insensitive) |
+| `match_count` | number | 5 | Maximum **documents** to return |
+| `mode` | string | `"docs"` | `"docs"` = full document results (recommended) |
+| `alpha` | number | 0.7 | Semantic weight (0 = FTS only, 1 = semantic only) |
+| `min_score` | number | 0.5 | Minimum cosine similarity threshold |
+| `max_bytes` | number | 200000 | Response size budget in bytes. Results are dropped whole (never truncated mid-document) once the budget is reached. The response includes `truncated: true` and `response_bytes` when the limit was hit. See "Response size limit" below. |
+
+**Response envelope fields:**
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `results` | array | Matched documents or chunks (see per-row fields below) |
+| `query` | string | The original query |
+| `mode` | string | Search mode used |
+| `match_count` | number | `match_count` value used |
+| `project_name` | string\|null | Project filter applied (if any) |
+| `truncated` | boolean | `true` when results were dropped to stay within `max_bytes` |
+| `response_bytes` | number | Actual bytes in the returned `results` array |
+
+**Per-result row fields (`docs` mode — the recommended default):**
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `document_id` | string | UUID of the matched document |
+| `doc_title` | string | Document title |
+| `doc_source` | string | Origin: `"file"`, `"paste"`, `"agent"` |
+| `doc_metadata` | object | Arbitrary JSON metadata |
+| `best_score` | number | Highest chunk relevance score (0–1) |
+| `best_chunk_heading_path` | string[] | Heading breadcrumb of the best-scoring chunk |
+| `full_content` | string | Reconstructed document content (may be partial — see `is_partial`) |
+| `chunk_count` | integer | Number of chunks in `full_content` |
+| `total_chars` | integer | Full document size in characters (always the whole doc, even when `is_partial` is true) |
+| `is_partial` | boolean | `true` when `full_content` contains only matched chunks + neighbours instead of the complete document. Triggered when the document exceeds the small-to-big threshold (default 40 000 chars). Use `getDocument` to retrieve the full text. |
+| `doc_updated_at` | string | ISO 8601 timestamp of the last document update |
+| `version_count` | integer | Number of archived versions (0 if never updated) |
+| `doc_project_ids` | string[] | Project UUIDs the document belongs to |
+
+**Response size limit (`max_bytes`):**
+
+200 KB is a safety ceiling that prevents runaway responses under unusual settings (e.g. very high `match_count`). Under normal usage the small-to-big retrieval path already keeps individual large-document results compact (matched chunks + neighbours only), so this limit is rarely reached.
+
+You can override it per-request if needed:
+```json
+{ "query": "deployment checklist", "max_bytes": 400000 }
+```
+
+See `docs/guides/configuration.md` → "Response size limit" for full details.
+
+---
+
+### Cloud Claude (claude.ai web)
+
+Claude.ai web can connect to the Supabase-hosted remote MCP (no local install):
+
+1. In Claude.ai: **Settings → Integrations → Add integration**
+2. Enter the MCP URL:
+   ```
+   https://mcp.supabase.com/sse?project_ref=<your-project-ref>
+   ```
+3. Authenticate with your Personal Access Token when prompted.
+
+> **Limitation**: The cloud Supabase MCP only supports **FTS keyword search** — no hybrid or
+> semantic search. For full hybrid search from the web, deploy the MCP server to Cloud Run
+> (see `docs/TODO.md` → "Remote HTTP MCP server").
+
+---
+
+## Path C — Shell CLI for local coding agents
+
+### What it is
+
+Modern local coding agents — Claude Code, OpenAI Codex CLI, opencode, OpenClaw, Hermes, and many others — all expose a **Bash tool** (or similar shell-execution tool) to their underlying model. If the agent's user grants the agent access to a checked-out Cerefox repo, the agent can read and write the knowledge base by running `uv run cerefox …` exactly the same way a human would.
+
+This is **not a separate Cerefox installation path** — it's the same Layer 2 access (Python REST + service-role key) that you already use as a human via the CLI. What's new is the *usage model*: the user authorizes a local agent to use that CLI on their behalf, instead of (or alongside) configuring MCP.
+
+When to choose Path C over Path A:
+
+- **No MCP setup friction** — the agent already has a Bash tool; no `.mcp.json`, no `claude mcp add`, no Claude Desktop config edits.
+- **One Cerefox checkout serves any number of local agents** — Claude Code, Codex CLI, opencode, etc. running in the same project all use the same `uv run cerefox …` commands.
+- **Best for power users who already use the CLI themselves** — the agent and the user share one mental model and one set of conventions.
+
+When Path A is still better:
+
+- Cleaner agent UX — named tool calls (`cerefox_search(...)`) read better in agent transcripts than `Bash("uv run cerefox search 'foo'")`.
+- Some agents may rate-limit or budget Bash calls separately from MCP calls.
+- Cloud-only agents (claude.ai, chatgpt.com) cannot use Path C at all — they have no Bash tool.
+
+### Prerequisites
+
+Same as **Path A-Local**:
+
+- [`uv`](https://docs.astral.sh/uv/getting-started/installation/) installed on your machine
+- Cerefox repository cloned locally (e.g. `/Users/yourname/src/cerefox`)
+- `.env` configured with `CEREFOX_SUPABASE_URL`, `CEREFOX_SUPABASE_KEY` (service-role / new secret key), and your embedding API key (`OPENAI_API_KEY`)
+
+Quick sanity check before pointing an agent at it:
+
+```bash
+cd /path/to/cerefox
+uv run cerefox search "any query"
+uv run cerefox list-projects
+```
+
+If both work for you, they'll work for the agent.
+
+### How to enable it for an agent
+
+The pattern is the same across Claude Code, Codex CLI, opencode, OpenClaw, Hermes, and similar tools:
+
+1. **Tell the agent the Cerefox checkout path** (e.g. via system prompt, project memory, or your agent's equivalent of `CLAUDE.md`).
+2. **Point the agent at the agent docs** in that checkout: `AGENT_GUIDE.md` and `AGENT_QUICK_REFERENCE.md`. These already describe what to read, what to write, and the audit/metadata conventions. They cover MCP usage; the CLI mapping is in `AGENT_GUIDE.md` ("Using Cerefox via the CLI").
+3. **Optionally**: add a one-line reminder in the agent's system prompt so the model defaults to using Cerefox proactively.
+
+Example system-prompt snippet (adapt for your agent — Claude Code's `CLAUDE.md`, Codex's `AGENTS.md`, opencode's project config, etc.):
+
+```
+You have access to a personal Cerefox knowledge base via a local CLI.
+
+- Path: /path/to/cerefox  (cd here before running commands)
+- Run any command with: uv run cerefox <subcommand>
+- Read AGENT_GUIDE.md and AGENT_QUICK_REFERENCE.md in that directory for
+  conventions, metadata rules, and the MCP-tool → CLI-command mapping.
+  Full per-flag reference: docs/guides/cli.md.
+
+Identify yourself on every call:
+- Writes (ingest, ingest-dir): pass --author "<your-name>" --author-type agent
+- Reads (search, get-doc, list-versions, list-projects, metadata-search,
+  get-audit-log): pass --requestor "<your-name>"
+
+When answering questions, search Cerefox first. When the user asks you to
+remember something, ingest it. Cite document titles for every claim drawn
+from the knowledge base.
+```
+
+### MCP tool ↔ CLI command mapping
+
+The agent docs are written around MCP tool names. **CLI flag names match MCP parameter names exactly** (kebab-cased) — short forms like `--project`, `--filter`, `--count`, `--update`, `--version` are accepted as aliases. Full per-flag reference: [`docs/guides/cli.md`](cli.md).
+
+| MCP tool | CLI command |
+|---|---|
+| `cerefox_search` | `uv run cerefox search "<query>" --match-count N --project-name <n> --metadata-filter '<json>' --requestor <name>` (CLI-only: `--mode`, `--alpha`, `--min-score`) |
+| `cerefox_ingest` (file) | `uv run cerefox ingest <path> --title <t> --project-name <n> --metadata '<json>' --update-if-exists\|--document-id <uuid> --source <s> --author <a> --author-type user\|agent` |
+| `cerefox_ingest` (paste) | `printf '...' \| uv run cerefox ingest --paste --title "<title>"` (same flags) |
+| `cerefox_get_document` | `uv run cerefox get-doc <document-id> --version-id <vid> --requestor <name>` |
+| `cerefox_list_versions` | `uv run cerefox list-versions <document-id> --requestor <name>` |
+| `cerefox_list_projects` | `uv run cerefox list-projects --requestor <name>` |
+| `cerefox_list_metadata_keys` | `uv run cerefox list-metadata-keys` |
+| `cerefox_metadata_search` | `uv run cerefox metadata-search --metadata-filter '<json>' --project-name <n> --requestor <name>` |
+| `cerefox_get_audit_log` | `uv run cerefox get-audit-log --document-id <id> --author <a> --operation <op> --since <iso> --until <iso> --limit N --json --requestor <name>` |
+
+### Path C verification prompts
+
+After pointing your agent at the repo, ask it:
+
+> "Run a Cerefox search for 'second brain'. What did you find?"
+> Expected: agent runs `uv run cerefox search "second brain"` via its Bash tool and reports results.
+
+> "Save a note titled 'Test Note' to Cerefox with the content '# Test\nThis is a Path C test.'"
+> Expected: agent runs `cerefox ingest --paste --title "Test Note"` (or equivalent) and reports the new document ID.
+
+> "List my Cerefox projects."
+> Expected: agent runs `uv run cerefox list-projects`.
+
+### Caveats
+
+- **Privilege level**: the CLI uses the **service-role key** (`CEREFOX_SUPABASE_KEY`), which bypasses Row Level Security. An agent with Bash access has the same full read/write power you do. Only enable Path C for agents you trust to act on your behalf — the same trust level you'd grant Cursor/Claude Code for editing your source code.
+- **Audit attribution**: Path C records `access_path = "cli"` in usage logs, distinct from `"local-mcp"` / `"remote-mcp"`. **Agents must set `--author <name> --author-type agent` on writes and `--requestor <name>` on reads** (or rely on `CEREFOX_AUTHOR_NAME` / `CEREFOX_AUTHOR_TYPE` / `CEREFOX_REQUESTOR_NAME` env vars). Without these flags, writes attribute to `"unknown"` / `"user"`, which under-reports agent activity. See the 2026-05-18 Decision Log Q2 entry for the design rationale (`author_type` is caller-declared on ambiguous channels — CLI and Edge Functions — but `access_path` is always derived from the code layer).
+- **Soft-delete is reachable; purge and restore are not** — by design. `cerefox delete-doc` is exposed on the CLI and sends documents to trash with an audit entry. **Permanent purge** (irreversible) and **restore from trash** (un-doing a destructive action) are intentionally web-UI-only and require human-in-the-loop confirmation. If an agent on Path C decides to delete content, it should surface that to the user explicitly so they can review and either restore or commit. See [`access-paths.md` → Destructive operations and the trust model](access-paths.md#destructive-operations-and-the-trust-model) for the full rationale and contributor guidance.
+- **Cross-doc links in content you ingest** become clickable when the user views them in the Cerefox web UI. Author them as `[Text](uuid)` (most stable), `[Text](docs/path.md)` (repo files), or `[Text](<Title With Spaces>)` (angle-bracket form — bare spaces break markdown). See [`AGENT_GUIDE.md` → "Writing linkable content"](../../AGENT_GUIDE.md#writing-linkable-content) for the full set of rules.
+- **One repo per machine**: the agent needs your checkout — there's no "Path C without a local clone". If you skip the local install entirely, Path A-Remote or Path B is the only option.
+- **No sandboxing beyond the agent's existing Bash sandbox**: the CLI is just shell. If your agent's tool framework restricts which commands run, allowlist `uv run cerefox …` explicitly.
+
+### Path C is configuration-free, but here's the per-agent footprint
+
+| Agent | Where to mention the Cerefox path |
+|---|---|
+| Claude Code | `CLAUDE.md` in the project, or `~/.claude/CLAUDE.md` globally. No MCP entry needed. |
+| OpenAI Codex CLI | `AGENTS.md` or the project's instructions file. |
+| opencode | Project config / agent system prompt. |
+| OpenClaw, Hermes, custom local agents | Whatever the tool's system-prompt / memory mechanism is. |
+
+There is nothing Cerefox-specific to install for the agent itself — just the repo + your `.env`.
+
+---
+
+## Custom agents (Python SDK)
+
+Use the Cerefox Python client directly for scripted or embedded agents:
+
+```python
+from cerefox.config import Settings
+from cerefox.db.client import CerefoxClient
+from cerefox.embeddings.cloud import CloudEmbedder
+from cerefox.retrieval.search import SearchClient
+
+settings = Settings()            # reads from .env
+client = CerefoxClient(settings)
+embedder = CloudEmbedder(
+    api_key=settings.get_embedder_api_key(),
+    base_url=settings.get_embedder_base_url(),
+    model=settings.get_embedder_model(),
+    dimensions=settings.get_embedder_dimensions(),
+)
+sc = SearchClient(client, embedder, settings)
+
+resp = sc.search_docs("what did I write about Rust?", match_count=5)
+for hit in resp.results:
+    print(f"[{hit.best_score:.2f}] {hit.doc_title}")
+    print(hit.full_content[:400])
+```
+
+---
+
+## Keeping both paths in sync
+
+Both paths use the same Postgres RPCs and the same stored embeddings, but embed queries
+independently. If you change the embedding model, **update both paths** before searching:
+
+1. Update `.env` + run `cerefox reindex` (re-embeds stored chunks via Python)
+2. Update the TypeScript constants in `supabase/functions/*/index.ts` + redeploy Edge Functions
+
+See `docs/guides/configuration.md` → "Changing the embedding model" for the full procedure.
+
+---
+
+## MCP tool reference
+
+### `cerefox_search`
+
+Search the knowledge base. Returns complete documents ranked by hybrid (FTS + semantic) relevance.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `query` | string | required | Natural-language search query |
+| `match_count` | integer | 5 | Maximum **documents** to return |
+| `project_name` | string | optional | Filter to a specific project |
+
+Each result includes `doc_title`, `best_score`, `full_content`, `chunk_count`, `total_chars`, and `is_partial`. When `is_partial` is true, the document exceeded the small-to-big threshold: `full_content` contains the best-matching chunks and their neighbours rather than the whole document. The heading for such results includes a `— partial (N of M chars)` annotation. Use `cerefox_get_document` to retrieve the full text when needed.
+
+### `cerefox_ingest`
+
+Save a note or document to the knowledge base.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `title` | string | required | Document title |
+| `content` | string | required | Markdown content |
+| `document_id` | string | optional | UUID of an existing document to update. When provided, updates that document directly regardless of `update_if_exists`. Returns an error if the document does not exist. Workflow: `cerefox_search` → note `[id: ...]` → pass here. |
+| `project_name` | string | optional | Assign to a project (created if absent) |
+| `source` | string | `"agent"` | Origin label |
+| `metadata` | object | `{}` | Arbitrary JSON metadata |
+| `update_if_exists` | boolean | `false` | When true, update an existing document with the same title instead of creating a new one. The previous version is archived automatically. Content is re-indexed only if it changed. Ignored when `document_id` is provided. |
+
+### `cerefox_list_metadata_keys`
+
+No parameters. Returns all distinct metadata keys currently in use across documents, with document counts and up to 5 example values per key.
+
+### `cerefox_get_document`
+
+Retrieve the full reconstructed content of a document. Pass `version_id` to retrieve an archived version; omit it for the current version. Version UUIDs are returned by `cerefox_list_versions`.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `document_id` | string | required | UUID of the document to retrieve |
+| `version_id` | string | optional | UUID of a specific archived version; omit for current |
+
+### `cerefox_list_versions`
+
+List all archived versions of a document, newest first. Returns `version_id` (use with `cerefox_get_document`), `version_number`, `source`, `chunk_count`, `total_chars`, and `created_at`.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `document_id` | string | required | UUID of the document whose version history to list |
+
+---
+
+## RPC reference
+
+All RPCs are defined in `src/cerefox/db/rpcs.sql`.
+
+### Search RPCs
+
+Every chunk-level RPC returns these fields:
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `chunk_id` | UUID | ID of the matching chunk |
+| `document_id` | UUID | ID of the parent document |
+| `chunk_index` | INT | Position within the document |
+| `title` | TEXT | Chunk heading (H1/H2/H3) |
+| `content` | TEXT | Full chunk text |
+| `heading_path` | TEXT[] | Breadcrumb: e.g. `["Doc Title", "Section", "Sub"]` |
+| `heading_level` | INT | 0–3 |
+| `score` | FLOAT | Relevance score (higher = more relevant) |
+| `doc_title` | TEXT | Parent document title |
+| `doc_source` | TEXT | Origin: `"file"`, `"paste"`, `"agent"` |
+| `doc_project_ids` | UUID[] | Project UUIDs assigned to the document |
+| `doc_metadata` | JSONB | Document metadata |
+
+#### `cerefox_fts_search`
+
+Full-text keyword search. Does not require an embedding model.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_query_text` | TEXT | required | Keyword query |
+| `p_match_count` | INT | 10 | Results to return |
+| `p_project_id` | UUID | null | Filter by project |
+
+#### `cerefox_semantic_search`
+
+Vector similarity search. Requires a pre-computed query embedding.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_query_embedding` | VECTOR(768) | required | Query embedding |
+| `p_match_count` | INT | 10 | Results to return |
+| `p_use_upgrade` | BOOL | false | Use upgrade embedding column |
+| `p_project_id` | UUID | null | Filter by project |
+| `p_min_score` | FLOAT | 0.0 | Minimum cosine similarity |
+
+#### `cerefox_hybrid_search`
+
+Combines FTS and semantic search via linear alpha blending. Two overloads (with/without `p_project_id`).
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_query_text` | TEXT | required | Query string for FTS |
+| `p_query_embedding` | VECTOR(768) | required | Query embedding |
+| `p_match_count` | INT | 10 | Results to return |
+| `p_alpha` | FLOAT | 0.7 | Semantic weight (0=FTS only, 1=semantic only) |
+| `p_use_upgrade` | BOOL | false | Use upgrade embedding column |
+| `p_project_id` | UUID | null | Filter by project |
+| `p_min_score` | FLOAT | 0.0 | Minimum cosine similarity |
+
+#### `cerefox_search_docs`
+
+Document-level search. Runs hybrid search internally, deduplicates by document, then returns up to
+`p_match_count` **distinct documents** with their full reconstructed content. **This is the
+recommended RPC for agent use** — agents receive complete notes, not isolated chunks.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_query_text` | TEXT | required | Query string for FTS |
+| `p_query_embedding` | VECTOR(768) | required | Query embedding |
+| `p_match_count` | INT | 5 | Max documents to return |
+| `p_alpha` | FLOAT | 0.7 | Semantic weight |
+| `p_project_id` | UUID | null | Filter by project |
+| `p_min_score` | FLOAT | 0.0 | Minimum cosine similarity |
+| `p_small_to_big_threshold` | INT | 40000 | Documents larger than this return matched chunks + neighbours instead of the full document. Set to `0` to always return full content. Change the DEFAULT in `rpcs.sql` to apply server-wide. |
+| `p_context_window` | INT | 1 | Neighbour chunks on each side of each matched chunk. `1` → up to 3 contiguous chunks per hit. `0` → matched chunks only. |
+
+Returns: `document_id`, `doc_title`, `doc_source`, `doc_metadata`, `doc_project_ids`,
+`best_score`, `best_chunk_heading_path`, `full_content`, `chunk_count`, `total_chars`,
+`doc_updated_at`, `version_count`, `is_partial`.
+
+`is_partial` is `TRUE` when the document exceeded `p_small_to_big_threshold` — in that
+case `full_content` contains matched chunks + up to `p_context_window` neighbours on each
+side, deduplicated and sorted by `chunk_index`. `total_chars` always reflects the full
+document size regardless of whether the result is partial.
+
+---
+
+### Document RPCs
+
+#### `cerefox_reconstruct_doc`
+
+Fetch a full document by ID, concatenating all chunks in order.
+
+| Parameter | Type | Description |
+|-----------|------|-------------|
+| `p_document_id` | UUID | Document to reconstruct |
+
+Returns: `document_id`, `doc_title`, `doc_source`, `doc_metadata`, `full_content`,
+`chunk_count`, `total_chars`
+
+#### `cerefox_context_expand`
+
+Small-to-big retrieval: given a set of chunk IDs, returns those chunks **plus their immediate
+neighbours** (±`p_window_size` chunks within the same document).
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_chunk_ids` | UUID[] | required | Array of chunk UUIDs from search results |
+| `p_window_size` | INT | 1 | Chunks to expand in each direction |
+
+Returns: `chunk_id`, `document_id`, `chunk_index`, `title`, `content`, `heading_path`,
+`heading_level`, `doc_title`, `is_seed` (TRUE for the original seed chunks)
+
+#### `cerefox_save_note`
+
+Create a document record directly. The note is stored but **not embedded** — use `cerefox-ingest`
+Edge Function instead for notes that need to be immediately searchable.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `p_title` | TEXT | required | Note title |
+| `p_content` | TEXT | required | Markdown content |
+| `p_source` | TEXT | `'agent'` | Origin label |
+| `p_project_id` | UUID | null | Project to assign |
+| `p_metadata` | JSONB | `{}` | Metadata (agent name, tags, etc.) |
+
+Returns: `id`, `title`, `created_at`
+
+---
+
+### Metadata RPCs
+
+#### `cerefox_list_metadata_keys`
+
+No parameters. Returns all distinct metadata keys currently in use across documents.
+
+| Column | Type | Description |
+|--------|------|-------------|
+| `key` | TEXT | Metadata key name |
+| `doc_count` | BIGINT | Number of documents using this key |
+| `example_values` | TEXT[] | Up to 5 sample values |
+
+This RPC derives keys from actual `doc_metadata` JSONB — no separate registry table.
+
+---
+
+## Response size
+
+Cerefox's default `max_response_bytes = 200000` is a safety ceiling; small-to-big retrieval
+keeps individual results compact so this limit is rarely reached in practice. If your MCP
+client has a lower context limit, reduce it via `CEREFOX_MAX_RESPONSE_BYTES` in your `.env`.