Everything else here is local: skills on your machine, a vault on your disk.
This puts a vault behind a URL so an agent elsewhere can search and write it.
One container, one vault, one API key. The vault stays plain markdown on a
mounted volume, so Obsidian still opens it. The container does no LLM work --
search and packing delegate to the existing graphrag/context_pack modules, and
the caller's agent does the thinking.
- obsidian_wiki/server.py: four vault functions, five REST routes and four MCP
tools as transport over them. Auth is one bearer key; the process refuses to
start without WIKI_API_KEY unless WIKI_ALLOW_ANONYMOUS=1. Every path is
resolved inside the vault or refused.
- Dockerfile, docker-compose.yml, .dockerignore, and a ghcr push on v* tags.
- New [server] extra; the core wheel stays dependency-free.
- docs/deployment.md, plus the WIKI_* vars in configuration.md and .env.example.
Requires mcp>=2.0: 2.0 renamed FastMCP to MCPServer, and session_manager only
exists once streamable_http_app() has been called -- a mounted sub-app's own
lifespan is ignored, so it is wired into the FastAPI lifespan by hand.
Static, idempotent postgres.sql output (wiki_pages/wiki_edges tables,
ON CONFLICT upserts) loadable via psql — no driver dependency needed.
Documents the format in README, README_TW, and docs/.
* chore(sync): ignore the regenerable graph cache
New vaults get `.graph-cache.json` in their .gitignore — it is derived data
that churns on every graph change and should never enter history.
An existing .gitignore is the user's file and is left byte-identical; the
command prints a tip instead of editing it.
* feat(graph): bridges, cohesion, paths, neighbourhoods and a betweenness cache
Brings the graph analyser up to the algorithm family graphify runs on code
graphs, in pure Python (no networkx/numpy — the package stays dependency-free):
- `bridges` — exact Brandes betweenness centrality. The pages that sit on the
most shortest paths; removing one fragments the vault.
- `cohesion` per community — intra-cluster edge density; < 0.15 with 5+ pages
marks a fragmented cluster.
- `--path A B` — shortest wikilink chain between two pages.
- `--around PAGE --depth N --direction in|out|both` — N-hop neighbourhood;
`--direction in` is the blast radius if the page were renamed or removed.
- `--diff-against` / `--snapshot` — compare against a previous `_insights.md`
snapshot (added/removed pages and links, newly connected, lost incoming).
- `suggested_questions` — derived from bridges, sink hubs, isolates and
low-cohesion clusters.
Two correctness fixes fall out of this:
- Vault bookkeeping files (`index`, `log`, `hot`, `_insights` at the vault
root, plus `_meta/` and `_readouts/`) are no longer graph nodes. They link
to nearly every page, so they dominated every degree and centrality ranking.
A nested `concepts/index.md` is still an ordinary page.
- Pages are now iterated in sorted order rather than filesystem order, so
results are reproducible across machines. That exposed a latent flaw in the
label-propagation fallback: a sequential sweep cascades one label along
chains and collapsed a barbell graph into a single community. Nodes are now
visited in a seeded shuffle — deterministic, and clusters survive.
Betweenness is O(V*E) and the only expensive step in the module (~43s on a
5,000-page vault, versus 0.13s to parse it and 0.03s for communities), so it
is memoised in `.graph-cache.json`. The cache key is a hash of the graph
topology rather than file mtimes, which makes a stale hit impossible by
construction: retargeting any link changes the key, while editing prose
without touching links keeps the cached result valid. The file is only
written when the computation actually exceeded 0.5s, so small and medium
vaults never accumulate one; it is bounded to 3 keys, written atomically,
and ignored if corrupt.
Sampled betweenness (k pivots) was measured as an alternative and rejected:
25-50x faster but only 60-90% top-10 overlap and wrong ordering even on a
38-page vault, which is not acceptable for a ranked list a human reads.
* fix(query): stop routing paths through index.md; answer structural questions
`graph-query` is the front door `wiki-query` calls first, and it built its
own graph in graphrag.py with its own page-selection rules, its own slug
helper and its own BFS. Those rules did not exclude the vault bookkeeping
files, and `index.md` links to every page — so almost any two pages looked
about two hops apart and the returned "connection" was meaningless:
owasp-agentic-quotes -> prismor-overview
before: owasp-agentic-quotes -> index -> arnav -> prismor-overview
after: owasp-agentic-quotes -> agentic-governance-maturity
-> prismor -> arnav -> prismor-overview
On a 38-page vault, 52 of 630 page pairs (8%) routed through a bookkeeping
file, and 51 of those were shorter than the real semantic path, so BFS
preferred them. The share grows with vault size.
graphrag now uses the shared page selection from graph_analysis and delegates
to its `shortest_path`, so there is one graph and one BFS in the codebase.
On top of that, `graph-query` now answers questions about the shape of the
vault, phrased in plain English, and returns them fully computed in a new
`graph` field (null for ordinary queries, so the response stays backwards
compatible):
impact "what breaks if I delete X" / "what depends on X"
bridges "which pages bridge my clusters" / "what would fragment my vault"
hubs "what's central" / "top hubs" / "my main topics"
clusters "what clusters do I have" / "how is my wiki organised"
surprising "surprising connections" / "unexpected links"
These are computed lazily: only `bridges` needs betweenness, so every other
intent stays as cheap as an ordinary lookup even on a 5,000-page vault
(<= 0.71s measured). A structural question that names an unresolvable page
falls back to ordinary retrieval rather than guessing.
* docs: document the structural intents, query modes and graph cache
- docs/cli.md: the new graph-analyse flags, the graph-query structural
questions, and a section on the cache (what it stores, why the key is the
graph topology, and when the file is written).
- wiki-query: route structural questions to graph-query and report the
`graph` payload directly instead of re-deriving it from page reads.
- wiki-status: insights mode now reads bridges, cohesion, suggested questions
and the graph delta straight from the analyser rather than instructing the
model to compute them by hand.
* docs(readme): add the structural-query benchmark vs a plain agent
Same model, same vault, same plain-English questions — the only difference is
whether obsidian-wiki is installed: 81s -> 19s, 44% -> 83% correct, at
unchanged API cost.
Includes the per-question breakdown and, in a collapsed block, the method and
its limits: ground truth verified against networkx rather than this project's
own code, n=2 per cell on a single 38-page vault, and the one run in the
"with" column that failed outright. The accuracy gap is attributed to its
actual cause — the plain agent routing through index.md, which links to every
page.
Both READMEs updated together per the translation-parity rule.
* test: add code-understanding fixtures (fake codegraph CLI, repo builder)
* feat: add code_understanding module with builtin + codegraph providers
Provider abstraction behind code_understand(): builtin uses the regex
ast_extractor plus rg cross-file references (dependency-free fallback);
codegraph shells out to the codegraph CLI with defensive JSON parsing.
Focus-map output is ranked symbols with file:line citations, capped by
max_symbols, and never contains source bodies.
* feat(cli): wire code-understand command and doctor code-understanding checks
New 'obsidian-wiki code-understand --project' subcommand emits the focus
map JSON; doctor --project gains 5 code-understanding capability checks
(builtin, rg, codegraph, codegraph-index, codegraph-fresh). Missing
optional CodeGraph reports warn (exit 0); explicit CODE_UNDERSTANDING_
BACKEND=codegraph with a broken backend fails (exit 1).
* feat(skills): add optional code-understanding focus-map step to wiki-update
Step 3b runs 'obsidian-wiki code-understand --since <last_commit_synced>'
between deciding what to distill and distilling. GUARD-soft-fails like
wiki-ingest Step 1c; mandates file:line citations for architectural
claims and a pruning rule that removes relationships no longer
supported by the codebase. Registers CODE_UNDERSTANDING_BACKEND and
CODE_UNDERSTANDING_CODEGRAPH_BIN in the llm-wiki env reference.
* docs: document CODE_UNDERSTANDING_BACKEND and code-understand command
* docs: add CodeGraph install steps; teach wiki-update to offer install
configuration.md gains a Setup subsection under Code understanding
(npm install -g @colbymchenry/codegraph + verify + CODE_UNDERSTANDING_
CODEGRAPH_BIN fallback). wiki-update Step 3b gains an optional offer:
when codegraph is missing and the user wants the enhanced backend, the
agent may install it (with consent) and re-run the step.
* docs(readme): note code-graph-aware /wiki-update (EN + zh-TW parity)
* docs(readme): clarify zh-TW /wiki-update codegraph note
* fix(codegraph): cap impact queries at 25 seeds on full-project scans
Full scans (no --changed/--since) seed from every tracked file, so an
unbounded impact loop fired one subprocess per symbol — hundreds of
codegraph CLI calls on real repos (observed 120s+ timeout on a 4.3k-node
project). Cap impact at 25 seeds, matching the existing callers/callees
cap (seeds[:5]), keeping full scans bounded while --changed/--since
delta scans stay exhaustive for their small seed sets.
Regression test: test_codegraph_caps_impact_queries_on_full_scan pins the
25-call ceiling (RED: 30 calls -> GREEN: <= 25).
* feat(skills): add standalone code-understand skill
Exposes the code-graph-assisted focus map directly to any coding
agent session, not just as wiki-update Step 3b — so it can be invoked
on demand ("help me understand this codebase", "what breaks if I
change X") independent of a wiki sync.
---------
Co-authored-by: ar9av <ar9avg@gmail.com>
The brain-capture extension only went one way: browser -> vault. This adds
the return path — read the form on the current page, answer what the vault
supports, and leave the rest blank — and folds both directions into a single
two-tab extension renamed from "Brain Vault Capture" to "Brain".
Retrieval never calls a model. `obsidian-wiki context-pack --json` ranks the
vault deterministically and the model does one narrow job: map retrieved facts
onto fields. One `claude -p` / `codex exec` invocation per fill, billed to the
subscription the user already has. Nothing is ever submitted.
A native messaging host bridges the two, staged into ~/.obsidian-wiki/ rather
than run from the checkout. Chrome's children do not inherit your shell, and
all three consequences bite:
- macOS TCC: ~/Documents is mode 700 with an ACL, and a native host inherits
Chrome's TCC context, so a checkout there cannot be exec'd at all. Chrome
reports this as "Native host has exited", identical to a crash.
- PATH: Chrome passes a minimal PATH, hiding claude/codex in ~/.local/bin.
- USER/LOGNAME: Claude Code reads OAuth credentials from the macOS login
Keychain and needs these to find them, else "Not logged in" despite a valid
session.
The host bookends every run in its log so those failures stay distinguishable,
re-validates every returned fill against the real form schema (an injected
value cannot reach a field the page never advertised), and forwards the pack's
instruction_policy so vault excerpts stay data rather than instruction.
Form-schema extraction resolves labels via aria-labelledby before aria-label:
Google Forms puts aria-label="Your answer" on every paragraph field while the
real question sits behind aria-labelledby, so checking aria-label first
silently mislabelled exactly the textarea fields. Values are written through
the native setter with input/change dispatched, so React-controlled forms see
a genuine edit.
Docs: docs/browser-extension.md, linked from both READMEs and the docs index.
Also backfills the untranslated tagline from #159 into README_TW.md.
Two strands of work.
Session brain — a topic graph over raw agent session history, so you can
find the session where something happened instead of remembering its
UUID. Reads every Claude transcript plus the pruned sessions that survive
only as prompts in history.jsonl, clusters them with local TF-IDF and
community detection (no embeddings, no API calls, no new dependencies),
and writes a sidecar at ~/.claude/session-brain/ — the vault is never
touched. Ships five modules, the sessions-* CLI commands, an interactive
graph.html, and the /session-brain and /wiki-sessions skills. This is
retrieval, deliberately distinct from wiki-history-ingest, which distils
sessions into permanent vault pages.
Docs — README.md was 598 lines and put trust-check flags and a 17-row
agent matrix in front of anyone evaluating the project. Cut it to a 129-
line landing page (problem statement, 60-second install, four blocks of
runnable commands, graph screenshot, why-not-a-notes-folder) and move the
reference material into docs/: installation, agents, skills, cli,
configuration, architecture, session-brain, contributing. README_TW.md
mirrors the new structure; docs/ stays English-only for now.
The restructure also closed real drift:
- Ten skills existed but appeared in no reference — session-brain,
session-search, wiki-dedup, wiki-digest, wiki-import, wiki-context-pack,
wiki-stage-commit, wiki-switch, vault-skill-factory, and
obsidian-layout-adjustment.
- SETUP.md listed 12 of 39 skills and still claimed "no scripts, no
dependencies" despite the pip package. It is now a signpost into docs/.
- Eight config variables were undocumented anywhere, including
WIKI_STAGED_WRITES, which wiki-setup prompts for and three skills read.
Added to .env.example and docs/configuration.md.
- sessions-name and a number of CLI flags were missing from the docs.
Two details worth noting. README links are absolute GitHub URLs because
pyproject sets readme = "README.md" as the PyPI long_description, and PyPI
resolves relative hrefs against pypi.org rather than the repo — docs/
links would have 404'd on the package page. And three doc-drift guards
asserted their facts against README.md; since those facts moved rather
than disappeared, the assertions were repointed at the page that now owns
each one instead of padding content back into the README.
Also gitignore /vault/ (a local knowledge vault, not a fixture) and the
packed browser extension.
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
setup.sh had an interactive git-sync flow (git init, .gitignore, remote,
a generated sync.sh, optional cron) that `obsidian-wiki setup` — the entry
point pip/uv installs actually run — never had, so those installs silently
skipped it and .env.example documented a var nothing ever read.
Move the git plumbing into obsidian_wiki/sync.py (configure_sync/run_sync/
get_remote) and expose it as `obsidian-wiki sync-setup <url>` and
`obsidian-wiki sync`. `obsidian-wiki setup` now offers the same interactive
prompt setup.sh always had (or accepts --remote non-interactively), and
setup.sh's own prompt delegates into the same module via the CLI instead of
re-implementing it. Sync status is read live from the vault's own `git
remote` (via `obsidian-wiki info`) rather than a config var that could drift.
The readme-sync workflow no longer fails when README.md and
README_TW.md don't change together. Instead, check_readme_sync.py
reports drift: it lists commits that touched README.md after the
last README_TW.md update, plus the pending English diff to translate
and backfill. CI surfaces drift as a warning annotation only.
Claude-Session: https://claude.ai/code/session_01PG9Pz6tcUfgpTHLjq3BT5Q
Reject symlinked writes and malformed or ambiguous trust data, enforce complete page coverage and strict timestamps/lifecycle values, and parse typed relationships independent of key order.
wiki-narrate saves derived readouts to _readouts/, but cross-linker,
wiki-export, and wiki-lint scanned every .md in the vault and would
have linked, exported, or lint-flagged them. Exclude the directory in
all three and document it in the AGENTS.md vault structure.
Continues the skill-surface consolidation (#84). Removes three skills
whose capability fully overlaps a survivor, so users and the router stop
disambiguating near-duplicates. No functionality lost.
- obsidian-wiki-ingest: a self-described "wrapper for wiki-ingest" that
never did anything wiki-ingest doesn't. Deleted outright.
- wiki-quick-chat-capture -> wiki-capture --quick: quick mode folded in
as a documented fast path (gate, _raw/ staging, <60s, no manifest
writes). RAW-FORMAT.md moved to wiki-capture/references/. The
session-end Stop hook now asks for `/wiki-capture --quick`.
- ingest-url -> wiki-ingest: URL ingestion folded in. The full URL
mechanics (project detection, defuddle, dedup, slug, project/misc
frontmatter, affinity scoring, stub handling, INGEST_URL log) moved
verbatim to wiki-ingest/references/url-sources.md, pointed to from a
new "Web URL sources" section.
Repointed every reference: AGENTS.md (+CLAUDE.md symlink), README,
wiki-setup, wiki-query, llm-wiki, RAW-FORMAT.md.
data-ingest was effectively wiki-ingest plus a format-detection
preamble — its own process step said "Follow the wiki-ingest skill's
process for creating/updating pages". The split forced users and the
skill router to disambiguate two overlapping ingest skills (a .md
ChatGPT export fit either one).
Fold it in to keep the skill surface small:
- wiki-ingest now handles structured docs AND raw/unstructured text
(chat exports, Slack/Discord JSON, CSV/JSON, transcripts, logs).
- Added an "Unstructured & conversational sources" section to Step 1
with format detection, chat-export shapes, and "distill substance,
not dialogue" guidance carried over from data-ingest.
- Expanded the description to absorb data-ingest's triggers.
- Removed .skills/data-ingest/ and repointed every reference
(CLAUDE.md/AGENTS.md, README, SETUP, llm-wiki, wiki-status,
wiki-rebuild, wiki-quick-chat-capture, and the mirror rule files
for cursor/windsurf/agent/kiro/copilot).
Adds an optional GitHub sync step to setup.sh that mirrors the common
`brainsync` alias pattern but reads vault path from ~/.obsidian-wiki/config.
- Prompts during setup: repo URL, shell alias, optional hourly cron
- git-inits vault if needed, writes .gitignore for Obsidian workspace files
- Writes ~/.obsidian-wiki/sync.sh (idempotent, skips if nothing staged)
- Adds wiki-sync alias to .zshrc/.bashrc on confirmation
- Summary line shows wiki-sync if sync was configured
- README: new "Syncing your vault to GitHub" section with manual setup notes
- .env.example: documents VAULT_GITHUB_REMOTE config key
* feat(pypi): package obsidian-wiki as a pip-installable distribution (#71)
Add a PyPI package so users can install without cloning the repo.
- pyproject.toml (hatchling, no runtime deps); force-include .skills/ and
bootstrap files into the wheel under obsidian_wiki/_data/ — repo root stays
the single source of truth. Force-include .skills/ into the sdist too, or
hatchling's VCS walker drops it (the committed agent symlink mirrors shadow
the real .skills/<name> files).
- obsidian_wiki CLI: Python port of setup.sh. `obsidian-wiki setup` writes
~/.obsidian-wiki/config and symlinks all skills into every supported agent
(--copy / --project / --project-only); plus `list` and `info`.
- .github/workflows/publish.yml: build + twine check + skill-bundle assertion,
publish to PyPI on v* tags via Trusted Publishing (OIDC).
- README + SETUP: pip install instructions; gitignore build artifacts.
* build(pypi): derive version from git tag via hatch-vcs; skip-existing on publish
Align the package version with the repo's CalVer release tags (v2026.05.2 ->
2026.5.2) so tagging a release is the version bump and future release tags
auto-publish the matching version.
Thanks for the well-structured PR — mirrors the existing `claude-history-ingest` / `codex-history-ingest` pattern cleanly and the Pi session-format details (tree JSONL with id/parentId, message roles, compaction/branch_summary) line up with pi.dev.
Reviewed:
- New `pi-history-ingest` skill, routing across `wiki-history-ingest`, `wiki-agent` (`/wiki-pi`), and `memory-bridge`
- `setup.sh`, `.env.example`, `AGENTS.md`, `README.md`, `SETUP.md`, and all four IDE rule files updated consistently
- 38 committed symlinks under `.pi/skills/` + 5 cross-agent symlinks
One small follow-up: the SKILL.md cites `references/pi-data-format.md` but the file isn't shipped (the claude/codex skills both ship that companion reference). I'll add it in a follow-up so the family stays consistent.
- Add hot.md update step to 6 previously missing write skills:
cross-linker, tag-taxonomy, claude/codex/hermes/openclaw-history-ingest
- New wiki-synthesize skill: scans vault for concept pairs that
co-occur across pages but lack a synthesis/ page, scores candidates,
drafts cross-cutting synthesis pages with A × B title format
- wiki-lint check #11: synthesis gap report with co-occurrence counts
- CLAUDE.md routing + README skills table updated
- wiki-capture: save any conversation as a permanent wiki note; classifies into 5
types (synthesis/concept/source/decision/session) and rewrites content as
declarative knowledge rather than a chat transcript
- wiki-research: autonomous 3-round web research loop that decomposes topics,
fills gaps, resolves contradictions, and self-files into sources/concepts/
entities/synthesis
- wiki-dashboard: creates Obsidian Bases .base files (native, no plugin needed)
for dynamic queryable views — tables, cards, lists filtered from vault frontmatter
- hot.md session cache: ~500-word semantic snapshot of recent activity; all write
skills (wiki-ingest, wiki-update, ingest-url, data-ingest) now update it at the
end of each run; wiki-query reads it first for cheap context
- ingest-url: preflight check for defuddle CLI — uses it for cleaner URL extraction
when available (~40-60% token reduction on articles), falls back to WebFetch
- Routing table in AGENTS.md updated; symlinks created across all 5 platforms
Rewrites .obsidian/graph.json colorGroups from the vault's real vocabulary.
Backs up the existing file and only touches colorGroups so user zoom/physics/filter
prefs stay intact. Modes: by-tag (default), by-category, by-visibility, combined, custom.
Aligns obsidian-wiki's install surface with graphify's supported platforms:
- Kiro IDE/CLI: adds .kiro/steering/obsidian-wiki.md (inclusion: always) and
.kiro/skills/ as a symlink target
- Google Antigravity: adds .agent/rules/obsidian-wiki.md (alwaysApply) and
.agent/workflows/obsidian-wiki.md as the slash-command registry
- setup.sh: adds global skill symlinks for Copilot CLI (~/.copilot/skills),
Trae (~/.trae/skills), Trae CN (~/.trae-cn/skills), Kiro (~/.kiro/skills),
and the canonical Gemini CLI path (~/.gemini/skills); keeps the legacy
~/.gemini/antigravity/skills path for backwards compat
- README.md and SETUP.md: expand the Agent Compatibility matrix from 9 rows
to 17 (Gemini CLI split from Antigravity; OpenCode, Aider, Droid, Trae,
Trae CN, Kiro, Copilot CLI added) and add <details> setup blocks for each
new platform
Arnav