brain-wiki 0.1.0__tar.gz

brain_wiki-0.1.0/.claude-plugin/marketplace.json

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+{
+  "name": "brain-wiki",
+  "owner": {
+    "name": "brain-wiki contributors"
+  },
+  "description": "brain-wiki: a local-first Markdown second brain shared by your AI agents.",
+  "version": "0.1.0",
+  "plugins": [
+    {
+      "name": "brain-wiki",
+      "source": "./",
+      "description": "A local-first second brain for AI agents, kept as plain Markdown that you own.",
+      "category": "productivity"
+    }
+  ]
+}

brain_wiki-0.1.0/.claude-plugin/plugin.json

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+{
+  "name": "brain-wiki",
+  "displayName": "brain-wiki",
+  "version": "0.1.0",
+  "description": "A local-first second brain for AI agents, kept as plain Markdown that you own.",
+  "author": {
+    "name": "brain-wiki contributors"
+  },
+  "repository": "https://github.com/brain-wiki/brain-wiki",
+  "license": "Apache-2.0",
+  "keywords": [
+    "memory",
+    "agents",
+    "mcp",
+    "markdown",
+    "obsidian",
+    "knowledge-base"
+  ]
+}

brain_wiki-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.venv/
+build/
+dist/
+
+# Tooling caches
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.coverage
+htmlcov/
+
+# Editors and OS
+.idea/
+.vscode/
+.DS_Store
+
+# Local only: drafts, test caches, and the lockfile (dependencies resolve from pyproject.toml)
+.scratch/
+.hypothesis/
+uv.lock

brain_wiki-0.1.0/.mcp.json

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+{
+  "mcpServers": {
+    "brain-wiki": {
+      "type": "stdio",
+      "command": "uvx",
+      "args": [
+        "--from",
+        "brain-wiki==0.1.0",
+        "brain",
+        "mcp",
+        "--host",
+        "auto"
+      ]
+    }
+  }
+}

brain_wiki-0.1.0/.pre-commit-hooks.yaml

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+- id: brain-lint
+  name: brain-wiki lint
+  description: Check staged brain files against the brain-wiki format.
+  entry: brain lint --staged
+  language: python
+  pass_filenames: false
+  files: '(\.md|brain\.toml)$'

brain_wiki-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2026-10-14)
+
+The first release of the 0.1 line. brain-wiki is alpha: expect breaking
+changes before 1.0. Changes since 0.1.0.dev1:
+
+- `brain obsidian [BRAIN]` opens the brain's folder as a vault in Obsidian,
+  adding it as a new vault the first time through the Obsidian CLI (or, without
+  the CLI, opening the vault manager with the step to take).
+- `brain viz [BRAIN]` and `brain obsidian [BRAIN]` open the named brain, the
+  only brain, or with several, the one you pick from a list (the usual brain is
+  the default).
+- `brain setup` asks first whether to create a new brain or adopt a folder you
+  have, names the brain after its folder, and shows the answer Enter picks
+  for every question.
+
+## 0.1.0.dev1 (2026-10-14)
+
+- `brain setup --guide` prints the setup steps for an AI agent, so any agent
+  that can run commands can set brain-wiki up from one prompt, without the
+  plugin. Without a terminal, `brain setup` points to it, and an agent that
+  finds no brain is told to use the `brain-setup` skill or the guide.
+- Every setup step is now a command, so the guide never edits config files:
+  `brain agents [list | grant | revoke]` changes what an app may do as an
+  undoable run, and `brain harvest enable | disable | route` configures
+  harvest. A refusal names the `brain agents grant` command that allows it.
+  `brain brains limit HOST BRAIN...` and `unlimit HOST` set which brains an
+  app may use.
+- `brain setup` also asks what each connected app may do, grants the
+  `harvest` ability with harvest, and ends with what to try next.
+- The CLI is built on Typer. Action commands are real subcommands with their
+  own help (`brain rules add --help`), and `brain --install-completion`
+  installs tab completion. `--brain`, `--as`, and `--json` still work before
+  or after the command. `brain --version` also prints the file format.
+- Removed commands, and what replaces them: `brain version` → `brain
+  --version`; `brain list` → `brain brains` (also with `--as HOST`); `brain
+  notes` and `brain recent` → `brain search ""` with filters (e.g. `brain
+  search "" --since 7d`; browsing sorts by `recent`); `brain outline TARGET` →
+  `brain read TARGET --mode outline`.
+- `brain rule` is now `brain rules`; `rule` still works as a hidden alias.
+- `brain review` also covers rule proposals: `review list` shows them with
+  consolidation and edit proposals, marking each one's kind, and `review
+  show`, `accept`, and `reject` take a rule proposal's id.
+- `brain import --phase` given with a mode other than `--overlay` is a usage
+  error even when it is `--phase 0`.
+- Harvest routes are a fallback: a project's `.brain-wiki.toml` now wins over
+  a catch-all route such as `~/**`.
+
+Fixes from an audit of every command, each with a regression test:
+
+- **Data loss:** undo could delete notes when the first write came before
+  any full scan. In a git brain, undo lost files git never tracked (inbox
+  episodes, proposals), left deletions staged, and failed for any run but the
+  newest. Undo now restores from the run's saved copies in every brain.
+- **Safety:** `brain review accept` trusted the packet inside the proposal
+  file, so a forged one could write `rules.md`; it now rebuilds the packet
+  from the brain. `--as HOST` is enforced by every write command.
+- `brain import --apply --dry-run` applied the import; a failed `brain
+  brains rename` deleted the brain's entry; overlay phases 1–3 never ran in
+  a git repository; `--to-episodes` turned frontmatter into an episode.
+- `tags`, `types`, `orphans`, and `unresolved` showed a stale index; `search
+  --where` ignored tags, aliases, title, and id; `read --mode raw` was not
+  the raw file; `doctor` counted hubs as notes.
+- `brain check` recorded edits that lint rejects; `brain mv` of a topic left
+  its `brain.toml` entry behind; topics with `review = "always"` skipped
+  review for new notes.
+- `brain connect` broke a project-scope install on a later user-scope
+  connect, did not restore config files byte for byte, and crashed on
+  malformed JSON.
+- Unexpected errors exit 10 with a log reference instead of a traceback;
+  conflicts report `conflict:`, and only stale data reports `stale:`.
+
+## 0.1.0.dev0 (2026-10-14)
+
+First release.
+
+- **Brain format**: plain Markdown notes with frontmatter, claims with
+  provenance, and typed relations (`part_of`, `depends_on`,
+  `conflicts_with`, `supersedes`, `related_to`, and their inverses);
+  topics as folders, nested to any depth; immutable inbox episodes;
+  `rules.md`; a managed `AGENTS.md` block.
+- **Index and retrieval**: SQLite FTS5 index outside the brain, freshness
+  checks, guard co-retrieval (superseding and conflicting notes come with
+  every hit), search filters, facets, and intents, orientation, and
+  Obsidian-style browsing (`brain topics`, `notes`, `links`, `backlinks`,
+  `tags`, and more).
+- **Write path**: one episode writer with server-set provenance, secret
+  redaction, size caps, and dedupe; episodes dropped in by hand count as
+  untrusted; checked direct edits (`brain check`, `brain restore`, a
+  per-topic `agent_edits` policy), which agents may make by default; rules
+  that need the user's words and confirmation; `brain mv`.
+- **Runs**: every curated change is locked, gated by lint, recorded with
+  pre-images, committed to git when the brain is a repository, and
+  undoable.
+- **Consolidation**: packets with short handles, a per-op validator, a
+  deterministic writer that never deletes text, and review proposals. Your
+  agent consolidates in its session over MCP; `brain consolidate --prepare`
+  and `--apply` drive it by hand.
+- **Lint and reports**: the BW rule catalog with strict and migrate
+  profiles, cached whole-brain lint, safe fixes as one run, staged-file
+  lint and a pre-commit hook, and browsable reports.
+- **Agents**: a stdio MCP server with thirteen tools and three prompts;
+  `brain connect` for Claude Code, Codex, Antigravity, OpenClaw, and
+  Cursor, with instructions placed where each host reads them; session readers and
+  harvest for Claude Code, Codex, and Antigravity, with headless presets
+  for large backfills; origin lookup; a plugin bundle with three skills;
+  `brain setup` and `brain doctor`.
+- **Import**: overlay adoption of Obsidian vaults in phases, copying into
+  a brain, documents and agent memory files as episodes.
+- **Visualizer**: `brain viz`, a local read-only 3D map of groups,
+  topics, folders, and notes with typed relations and issue highlighting,
+  and HTML, JSON, and GraphML export.
+- **Bench**: offline retrieval, lint, and performance suites, and
+  model-backed consolidation scenarios through headless presets.
+
+Known limitations:
+
+- No privacy levels inside a brain: every agent that may use a brain
+  reads all of it. Keep separate lives in separate brains
+  ([proposal](https://github.com/brain-wiki/brain-wiki/blob/main/docs/proposals/privacy.md)).
+- Maintenance runs when you ask your agent; there is no scheduler
+  ([proposal](https://github.com/brain-wiki/brain-wiki/blob/main/docs/proposals/scheduled-maintenance.md)).
+- Chat apps that need a remote MCP server (ChatGPT, claude.ai, the Gemini
+  app) are not supported ([proposal](https://github.com/brain-wiki/brain-wiki/blob/main/docs/proposals/remote-mcp.md)).

brain_wiki-0.1.0/CONTRIBUTING.md

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+# Contributing to brain-wiki
+
+## Setup
+
+```sh
+uv sync                      # creates .venv with dev dependencies
+uv run brain --help
+```
+
+## Checks
+
+```sh
+uv run scripts/check.py      # everything CI runs: lint, format, tests, plugin sync, docs brain, visualizer bundle, package contents
+uv run pytest -q             # tests only
+uv run ruff format src tests scripts && uv run ruff check src tests scripts   # format, then lint
+```
+
+After editing `docs/`, regenerate the docs brain (`docs-brain/`, the docs as a
+brain) with `uv run scripts/build_docs_brain.py`; CI fails when it is stale.
+After changing the version or anything under `src/brainwiki/assets/`, run
+`uv run scripts/sync_versions.py`.
+
+### The visualizer front end
+
+`brain viz` serves a prebuilt bundle from `src/brainwiki/viz/app/`, so users
+never need Node. Its source is the
+[brain-wiki-viz](https://github.com/brain-wiki/brain-wiki-viz) repository.
+Clone it next to this one, then:
+
+```sh
+cd ../brain-wiki-viz
+npm ci                       # Node 20.19+, or 22.12+ on Node 22
+npm run check                # type check, unit tests, lockfile check
+git commit …                 # commit the source first: the build records its commit
+npm run build                # writes ../brain-wiki/src/brainwiki/viz/app/
+```
+
+Commit the rebuilt bundle here. `scripts/check.py` checks that the bundle is
+complete and was built from a clean brain-wiki-viz commit
+(`BUILD_INFO.json`); `scripts/check_viz.py --source ../brain-wiki-viz`
+also rebuilds that checkout and fails if the result differs. For live reload,
+run `brain viz --no-open --port 8765` here and `npm run dev` there, then open
+the dev server with the token from `brain viz` (`?t=…`).
+
+## Releasing
+
+CI (`.github/workflows/ci.yml`) runs `scripts/check.py` on Linux and macOS
+with Python 3.11 and 3.13, runs brain-wiki-viz's checks at the bundle's
+commit, and checks that the bundle rebuilds from it. A version tag runs
+`.github/workflows/release.yml`: it checks the tag against the version and
+the changelog, runs the checks, builds, publishes to PyPI with trusted
+publishing, and creates the GitHub release from the changelog entry. Its
+MCP Registry job is turned off until the project decides to be listed.
+
+1. Set `version` in `pyproject.toml` to `X.Y.Z`, or a development release
+   such as `X.Y.Z.devN`, and date its changelog entry: `## X.Y.Z (YYYY-MM-DD)`.
+   A development release goes to PyPI like any other, and pip and uv install
+   it while no final release exists. The GitHub release follows the same
+   rule: it is marked Latest until a final release exists, and a
+   pre-release after that.
+2. `uv run scripts/sync_versions.py`, then commit.
+3. `git tag vX.Y.Z && git push origin main vX.Y.Z`.
+4. Move `main` to the next development version (`X.Y.(Z+1).dev0` after
+   `X.Y.Z`, `X.Y.Z.dev(N+1)` after `X.Y.Z.devN`) with a new `(unreleased)`
+   entry, run `sync_versions.py`, commit, and push. The plugin files keep
+   pointing at the newest dated release, because marketplaces install the
+   plugin from `main`.
+
+One-time setup: a trusted publisher on PyPI for this repository, workflow
+`release.yml`, environment `pypi` (and that environment in the GitHub
+repository settings); private vulnerability reporting turned on (see
+`SECURITY.md`).
+
+## Where things are
+
+| Path | What |
+|---|---|
+| `docs/design/` | The design of what is implemented. Read the relevant document before changing behavior, and update it in the same change. |
+| `docs/proposals/` | Designs not yet built, and the backlog. Building one moves its content into `docs/design/`. |
+| `src/brainwiki/` | The package (layout in `docs/design/13-engineering.md` §2) |
+| `src/brainwiki/assets/` | Prompts the engine uses; the skills' copies are generated from them |
+| `plugin.json`, `mcp.json`, `.mcp.json`, `mcp_config.json`, `rules/`, `skills/`, `.claude-plugin/`, `server.json` | The plugin, served from the repository root. These names, and `hooks/` and `hooks.json`, are reserved by hosts; the bundle ships no hooks. |
+| `src/brainwiki/viz/app/` | The visualizer's built bundle (source: brain-wiki-viz); do not edit by hand |
+| `scripts/sync_versions.py` | Writes the version into every manifest and regenerates skill references (`--check` in CI) |
+| `tests/fixtures/` | Synthetic fixtures only |
+
+## Rules
+
+- **No real personal data anywhere**: examples and fixtures use the
+  fictional notes app "Lumen" and generic paths.
+- **Test fixtures never contain credentials**, even fake ones in their real
+  shape; build such strings at runtime in the test.
+- **Minimal visibility.** Modules inside a package are private
+  (`_name.py`); a package's API is what its `__init__.py` re-exports, and
+  code outside the package imports only that (tests may reach private
+  modules). Inside a module, a name is public only when another module, a
+  test, or a script uses it. `scripts/check_visibility.py` (part of
+  `scripts/check.py`) enforces both; `docs/design/13-engineering.md` §2 has
+  the details.
+- **Writers never reflow text.** Anything that edits a note changes only the
+  lines it must; add a test that untouched lines survive byte for byte.
+- **Every curated change goes through `runs.Run`** so it is recorded,
+  locked, gated by lint, and undoable.
+- **The CLI starts fast**: subcommand modules are imported lazily, and only
+  `brain mcp` imports the MCP SDK (`docs/design/07-interfaces.md` §2.4).
+- One version number, in `pyproject.toml`; run `scripts/sync_versions.py`
+  after changing it or any file under `src/brainwiki/assets/`.
+
+## Commits and pull requests
+
+Conventional Commits (`feat(lint): …`, `fix(index): …`). The message says
+why the change exists, not what the diff shows.

brain_wiki-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
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brain_wiki-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: brain-wiki
+Version: 0.1.0
+Summary: A local-first second brain for AI agents, kept as plain Markdown that you own.
+Project-URL: Homepage, https://github.com/brain-wiki/brain-wiki
+Project-URL: Documentation, https://github.com/brain-wiki/brain-wiki/tree/main/docs/user
+Project-URL: Repository, https://github.com/brain-wiki/brain-wiki
+Project-URL: Issues, https://github.com/brain-wiki/brain-wiki/issues
+Project-URL: Changelog, https://github.com/brain-wiki/brain-wiki/blob/main/CHANGELOG.md
+Author: brain-wiki contributors
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: agents,knowledge-base,markdown,mcp,memory,obsidian
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Text Processing :: Markup :: Markdown
+Requires-Python: >=3.11
+Requires-Dist: filelock>=3.12
+Requires-Dist: jsonschema>=4.20
+Requires-Dist: mcp<3,>=2.3
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: tomlkit>=0.12
+Requires-Dist: typer<1,>=0.26
+Description-Content-Type: text/markdown
+
+<!-- mcp-name: io.github.brain-wiki/brain-wiki -->
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/brain-wiki/brain-wiki/main/.github/assets/logo.svg" alt="brain-wiki" width="96" height="96">
+</p>
+
+<h1 align="center">brain-wiki</h1>
+
+<p align="center"><strong>One long-term memory for all your AI agents, kept as plain Markdown that you own.</strong></p>
+
+<p align="center">
+  <a href="https://github.com/brain-wiki/brain-wiki/actions/workflows/ci.yml"><img src="https://github.com/brain-wiki/brain-wiki/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="https://pypi.org/project/brain-wiki/"><img src="https://img.shields.io/pypi/v/brain-wiki" alt="PyPI"></a>
+  <a href="https://pypi.org/project/brain-wiki/"><img src="https://img.shields.io/pypi/pyversions/brain-wiki" alt="Python"></a>
+  <a href="https://github.com/brain-wiki/brain-wiki/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-Apache--2.0-blue" alt="License"></a>
+</p>
+
+Your agents (Claude Code, Codex, Antigravity, Cursor, OpenClaw, or any MCP
+client) share one brain: a folder of Markdown notes they search before
+answering and keep up to date as they work. It runs on your machine, needs no
+server or API keys, and opens in Obsidian.
+
+- **Plain files.** Read, edit, diff, and sync the brain like any folder, or adopt an Obsidian vault as it is.
+- **Knows what changed.** Search returns a note together with the notes that replace or contradict it.
+- **Safe to let agents write.** Changes are checked, logged, and undoable, and committed when the brain is a git repository.
+- **No network calls.** Your own agent does the thinking; brain-wiki stores and checks.
+
+## Quick start
+
+Needs Python 3.11+ and [uv](https://docs.astral.sh/uv/).
+
+**1. Install.**
+
+```sh
+uv tool install brain-wiki
+```
+
+**2. Set it up.**
+
+- **Recommended:** paste this into your agent (Claude Code, Codex,
+  Antigravity, Cursor, OpenClaw, ...):
+
+  > Set up brain-wiki by running `brain setup --guide` and following it.
+
+- **Or, in a terminal:** run `brain setup`, which asks the same questions
+  step by step.
+
+Either way, setup explains each choice (where the brain lives, which agents to
+connect, what each may do) and shows every change before making it.
+
+**3. Use it in your agent.**
+
+> Remember that I prefer pnpm over npm, and that our team ships on Thursdays.
+
+> What did we decide about the database migration last week?
+
+> Maya moved to the platform team. Update her note.
+
+> Consolidate my brain.
+
+**4. See your brain.** `brain viz` opens a local 3D map of your notes, and
+`brain obsidian` opens the brain's folder as a vault in Obsidian. With several
+brains, both ask which one, or name it: `brain viz work`.
+
+## How it works
+
+```text
+agents ──log──► inbox ──consolidate──► notes (topics/*.md) ◄── you, in Obsidian
+  ▲                   (checked ops)            │
+  └────────────── search · read ───────────────┘
+```
+
+Agents log what they learn to an inbox. When you ask, your agent folds the
+inbox into topic notes through small operations that brain-wiki checks before
+writing, and `brain undo` reverses any change.
+
+## Status
+
+Alpha: expect breaking changes before 1.0. Known limits:
+
+- No access scopes inside a brain: every connected agent reads all of it. Keep work and personal notes in separate brains.
+- Maintenance runs when you ask; there is no scheduler.
+- Chat apps that need a remote MCP server (ChatGPT, claude.ai, the Gemini app) are not supported yet.
+
+## Learn more
+
+[Getting started](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/getting-started.md) ·
+[Agents](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/agents.md) ·
+[Maintenance](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/maintenance.md) ·
+[Import a vault](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/import.md) ·
+[Privacy](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/privacy.md) ·
+[Reference](https://github.com/brain-wiki/brain-wiki/blob/main/docs/user/reference.md) ·
+[Design](https://github.com/brain-wiki/brain-wiki/blob/main/docs/design/README.md) ·
+[Changelog](https://github.com/brain-wiki/brain-wiki/blob/main/CHANGELOG.md)
+
+[Contributing](https://github.com/brain-wiki/brain-wiki/blob/main/CONTRIBUTING.md) ·
+[Security](https://github.com/brain-wiki/brain-wiki/blob/main/SECURITY.md) ·
+[Apache 2.0](https://github.com/brain-wiki/brain-wiki/blob/main/LICENSE)
+([visualizer notices](https://github.com/brain-wiki/brain-wiki/blob/main/src/brainwiki/viz/app/THIRD_PARTY_NOTICES.txt))