obsidian-mcp-server 3.5.2 → 3.5.4

package/AGENTS.md

@@ -1,11 +1,11 @@
 # Agent Protocol
 
 **Server:** obsidian-mcp-server
-**Version:** 3.5.2
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.8`
-**Engines:** Bun ≥1.3.0, Node ≥24.0.0
+**Version:** 3.5.4
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
+**Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
-**Zod:** ^4.5.4
+**Zod:** ^4.6.5
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
 
@@ -167,6 +167,22 @@ export function getServerConfig() {
 
 `parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`OBSIDIAN_API_KEY`) rather than the internal path (`apiKey`). It throws a `ConfigurationError` the framework catches and prints as a clean startup banner.
 
+### Session posture and shutdown
+
+`src/index.ts` passes two `createApp()` options that shape how the server runs:
+
+```ts
+await createApp({
+  // ...
+  sessionMode: 'stateful',
+  teardown: () => obsidian.close(),
+});
+```
+
+`sessionMode: 'stateful'` is the default, not a requirement: `obsidian_delete_note` confirms through `ctx.requestInput`, which a 2025-era HTTP client can only answer on a stateful session. An explicit `MCP_SESSION_MODE` still wins, so an operator who deliberately runs `stateless` gets a working server whose delete confirmation is refused with `client_capability_missing` on those clients. Don't switch it to `require: 'stateful'`.
+
+`teardown` closes the undici `Agent` dispatcher `ObsidianService` holds for the Local REST API and Omnisearch, releasing its keep-alive sockets. It runs after the transport stops accepting requests, on every shutdown path.
+
 ---
 
 ## Context
@@ -189,7 +205,7 @@ The framework also provides `ctx.state`. It isn't used by this server — Obsidi
 
 Handlers throw — the framework catches, classifies, and formats.
 
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint that flows to the wire. Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text). Override with explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint that flows to the wire. Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text unless the message already contains it verbatim). Override with explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
 
 ```ts
 errors: [
@@ -278,9 +294,9 @@ src/
 
 ## Skills
 
-Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
+Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool. `bun run list-skills` prints the full registry. The directory is deliberately not `skills/`: Claude Code and Codex auto-load a plugin's root `skills/`, so a server that ships `.claude-plugin/` or `.codex-plugin/` would hand these development skills to every agent that installs it. Keep `skills/` free for skills meant for those agents.
 
-**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
+**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). Skills then load as context without referencing `framework-skills/` paths. After framework updates, run the `maintenance` skill — Phase B re-syncs the agent directory.
 
 Available skills:
 
@@ -300,7 +316,7 @@ Available skills:
 | `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
 | `git-wrapup` | Land working-tree changes as a commit stack — version bump, changelog, verify, commit by concern, release commit on top. No tag, no push to main; opens the release PR when the project declares release PR mode |
-| `release-pr-review` | Review pass on an open release PR — simplifier + correctness review, fixup commits autosquashed into the stack, PR body kept in sync. Release PR mode only |
+| `release-pr-review` | Review pass on an open release PR — simplifier + correctness review, fixes as ordinary commits on top of the stack, PR body kept in sync. Release PR mode only |
 | `release-and-publish` | Fast-forward merge (release PR mode) + tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
 | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
@@ -310,7 +326,7 @@ Available skills:
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
 | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
 | `api-config` | AppConfig, parseConfig, env vars |
-| `api-context` | Context interface, logger, state, progress |
+| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
 | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
 | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
@@ -320,7 +336,7 @@ Available skills:
 | `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
 | `api-workers` | Cloudflare Workers runtime |
 
-**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
+**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
 
 When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
 
@@ -336,13 +352,14 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
-| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
+| `bun run audit:fix` | `bun audit fix` — upgrade vulnerable packages to the lowest safe version within existing ranges (`--dry-run` previews, `--latest` rewrites ranges). First response when `devcheck` flags a transitive advisory; then `bun update <name>`, then `bun dedupe` |
+| `bun run audit:refresh` | Delete `bun.lock` and reinstall. Last resort after `audit:fix`, `bun update <name>`, and `bun dedupe` — re-resolves every ranged dep (the framework pin included) and rewrites the lockfile as `lockfileVersion: 2` |
 | `bun run tree` | Generate `docs/tree.md` |
 | `bun run list-skills` | Print project skill index (name, version, description) |
 | `bun run format` | Auto-fix formatting (safe fixes only) |
 | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
 | `bun run lint:mcp` | Validate MCP definitions against the linter rules |
-| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` |
+| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity, `user_config` wiring, plugin manifest identity and env contract (run by devcheck) |
 | `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
 | `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
 | `bun run start:stdio` | Production mode (stdio) — requires `bun run build` first |
@@ -350,13 +367,15 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run changelog:build` | Regenerate `CHANGELOG.md` rollup from `changelog/<minor>.x/*.md` |
 | `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 
+**CI is one file.** `.github/workflows/codeql.yml` is the only GitHub Actions workflow: CodeQL is GitHub-owned end to end, and the file runs only while the repo's CodeQL *default setup* is turned off. Verification — `devcheck`, tests, the release gates — runs locally; don't add a workflow that re-runs it.
+
 ---
 
 ## Bundling
 
-`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. MCPB is stdio-only — HTTP deployments are unaffected. Delete `manifest.json` and `.mcpbignore` if not shipping MCPB bundles; `lint:packaging` skips cleanly.
+`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`framework-skills/`, `skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. MCPB is stdio-only — HTTP deployments are unaffected. Delete `manifest.json` and `.mcpbignore` if not shipping MCPB bundles; `lint:packaging` skips cleanly.
 
-**Adding an env var requires both files:** `server.json` (`environmentVariables[]`) and `manifest.json` (`mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match.
+**Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match, that every `user_config` option is wired into `mcp_config.env` as `"X": "${user_config.X}"` (the host substitutes nothing else — `"${X}"` reaches the server as that literal string), and that an optional string option carries `"default": ""`. A user-supplied variable also goes into the plugin manifests: `.claude-plugin/plugin.json` `userConfig` + `${user_config.<option>}` in `env`, and `.codex-plugin/mcp.json` `env_vars`.
 
 ---
 
@@ -387,6 +406,25 @@ security: false                            # optional — true ONLY for a source
 
 ---
 
+## Publishing
+
+**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the changelog entry plus a gates section); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
+
+`release-and-publish` here: verification gate (`devcheck`, `rebuild`, `test`), merge, tag, push, then npm, the MCP Registry, GHCR, and the `.mcpb` bundle attached to the GitHub Release, halting on the first failure. The npm package is unscoped (`obsidian-mcp-server`). For reference, the underlying commands are:
+
+```bash
+bun publish --access public
+
+docker buildx build --platform linux/amd64,linux/arm64 \
+  -t ghcr.io/cyanheads/obsidian-mcp-server:<version> \
+  -t ghcr.io/cyanheads/obsidian-mcp-server:latest \
+  --push .
+
+bun run publish-mcp
+```
+
+---
+
 ## Imports
 
 ```ts
@@ -413,7 +451,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] If wrapping external API: tests include at least one sparse payload case with omitted upstream fields
 - [ ] Registered in `createApp()` arrays (directly or via barrel exports). Conditional registration (e.g. `commandToolDefinitions` behind `OBSIDIAN_ENABLE_COMMANDS`) happens in `src/index.ts`, not in the barrel
 - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
-- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
-- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
-- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name (never the npm scope — `lint:packaging` enforces this); `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; every user-supplied variable (API key, instance URL) is listed in `env_vars` so Codex forwards it from the user's environment. Never write `"KEY": ""` into `env` — an empty value replaces the user's exported key and is read as unset
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `author`, `repository`, `license`, `keywords` from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name. Every user-supplied variable is declared under `userConfig` (`type`, `title`, `description`; `sensitive: true` for keys and tokens; `required: true` or `default: ""`) and referenced from `env` as `"KEY": "${user_config.<option>}"` — mirror the `user_config` block in `manifest.json`. Never write `"KEY": ""` into `env`
 - [ ] `bun run devcheck` passes

package/CLAUDE.md

@@ -1,11 +1,11 @@
 # Agent Protocol
 
 **Server:** obsidian-mcp-server
-**Version:** 3.5.2
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.8`
-**Engines:** Bun ≥1.3.0, Node ≥24.0.0
+**Version:** 3.5.4
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
+**Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
-**Zod:** ^4.5.4
+**Zod:** ^4.6.5
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
 
@@ -167,6 +167,22 @@ export function getServerConfig() {
 
 `parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`OBSIDIAN_API_KEY`) rather than the internal path (`apiKey`). It throws a `ConfigurationError` the framework catches and prints as a clean startup banner.
 
+### Session posture and shutdown
+
+`src/index.ts` passes two `createApp()` options that shape how the server runs:
+
+```ts
+await createApp({
+  // ...
+  sessionMode: 'stateful',
+  teardown: () => obsidian.close(),
+});
+```
+
+`sessionMode: 'stateful'` is the default, not a requirement: `obsidian_delete_note` confirms through `ctx.requestInput`, which a 2025-era HTTP client can only answer on a stateful session. An explicit `MCP_SESSION_MODE` still wins, so an operator who deliberately runs `stateless` gets a working server whose delete confirmation is refused with `client_capability_missing` on those clients. Don't switch it to `require: 'stateful'`.
+
+`teardown` closes the undici `Agent` dispatcher `ObsidianService` holds for the Local REST API and Omnisearch, releasing its keep-alive sockets. It runs after the transport stops accepting requests, on every shutdown path.
+
 ---
 
 ## Context
@@ -189,7 +205,7 @@ The framework also provides `ctx.state`. It isn't used by this server — Obsidi
 
 Handlers throw — the framework catches, classifies, and formats.
 
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint that flows to the wire. Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text). Override with explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint that flows to the wire. Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text unless the message already contains it verbatim). Override with explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
 
 ```ts
 errors: [
@@ -278,9 +294,9 @@ src/
 
 ## Skills
 
-Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
+Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool. `bun run list-skills` prints the full registry. The directory is deliberately not `skills/`: Claude Code and Codex auto-load a plugin's root `skills/`, so a server that ships `.claude-plugin/` or `.codex-plugin/` would hand these development skills to every agent that installs it. Keep `skills/` free for skills meant for those agents.
 
-**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
+**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). Skills then load as context without referencing `framework-skills/` paths. After framework updates, run the `maintenance` skill — Phase B re-syncs the agent directory.
 
 Available skills:
 
@@ -300,7 +316,7 @@ Available skills:
 | `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
 | `git-wrapup` | Land working-tree changes as a commit stack — version bump, changelog, verify, commit by concern, release commit on top. No tag, no push to main; opens the release PR when the project declares release PR mode |
-| `release-pr-review` | Review pass on an open release PR — simplifier + correctness review, fixup commits autosquashed into the stack, PR body kept in sync. Release PR mode only |
+| `release-pr-review` | Review pass on an open release PR — simplifier + correctness review, fixes as ordinary commits on top of the stack, PR body kept in sync. Release PR mode only |
 | `release-and-publish` | Fast-forward merge (release PR mode) + tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
 | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
@@ -310,7 +326,7 @@ Available skills:
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
 | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
 | `api-config` | AppConfig, parseConfig, env vars |
-| `api-context` | Context interface, logger, state, progress |
+| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
 | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
 | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
@@ -320,7 +336,7 @@ Available skills:
 | `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
 | `api-workers` | Cloudflare Workers runtime |
 
-**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
+**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
 
 When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
 
@@ -336,13 +352,14 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
-| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
+| `bun run audit:fix` | `bun audit fix` — upgrade vulnerable packages to the lowest safe version within existing ranges (`--dry-run` previews, `--latest` rewrites ranges). First response when `devcheck` flags a transitive advisory; then `bun update <name>`, then `bun dedupe` |
+| `bun run audit:refresh` | Delete `bun.lock` and reinstall. Last resort after `audit:fix`, `bun update <name>`, and `bun dedupe` — re-resolves every ranged dep (the framework pin included) and rewrites the lockfile as `lockfileVersion: 2` |
 | `bun run tree` | Generate `docs/tree.md` |
 | `bun run list-skills` | Print project skill index (name, version, description) |
 | `bun run format` | Auto-fix formatting (safe fixes only) |
 | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
 | `bun run lint:mcp` | Validate MCP definitions against the linter rules |
-| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` |
+| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity, `user_config` wiring, plugin manifest identity and env contract (run by devcheck) |
 | `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
 | `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
 | `bun run start:stdio` | Production mode (stdio) — requires `bun run build` first |
@@ -350,13 +367,15 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run changelog:build` | Regenerate `CHANGELOG.md` rollup from `changelog/<minor>.x/*.md` |
 | `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 
+**CI is one file.** `.github/workflows/codeql.yml` is the only GitHub Actions workflow: CodeQL is GitHub-owned end to end, and the file runs only while the repo's CodeQL *default setup* is turned off. Verification — `devcheck`, tests, the release gates — runs locally; don't add a workflow that re-runs it.
+
 ---
 
 ## Bundling
 
-`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. MCPB is stdio-only — HTTP deployments are unaffected. Delete `manifest.json` and `.mcpbignore` if not shipping MCPB bundles; `lint:packaging` skips cleanly.
+`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`framework-skills/`, `skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. MCPB is stdio-only — HTTP deployments are unaffected. Delete `manifest.json` and `.mcpbignore` if not shipping MCPB bundles; `lint:packaging` skips cleanly.
 
-**Adding an env var requires both files:** `server.json` (`environmentVariables[]`) and `manifest.json` (`mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match.
+**Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match, that every `user_config` option is wired into `mcp_config.env` as `"X": "${user_config.X}"` (the host substitutes nothing else — `"${X}"` reaches the server as that literal string), and that an optional string option carries `"default": ""`. A user-supplied variable also goes into the plugin manifests: `.claude-plugin/plugin.json` `userConfig` + `${user_config.<option>}` in `env`, and `.codex-plugin/mcp.json` `env_vars`.
 
 ---
 
@@ -387,6 +406,25 @@ security: false                            # optional — true ONLY for a source
 
 ---
 
+## Publishing
+
+**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the changelog entry plus a gates section); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
+
+`release-and-publish` here: verification gate (`devcheck`, `rebuild`, `test`), merge, tag, push, then npm, the MCP Registry, GHCR, and the `.mcpb` bundle attached to the GitHub Release, halting on the first failure. The npm package is unscoped (`obsidian-mcp-server`). For reference, the underlying commands are:
+
+```bash
+bun publish --access public
+
+docker buildx build --platform linux/amd64,linux/arm64 \
+  -t ghcr.io/cyanheads/obsidian-mcp-server:<version> \
+  -t ghcr.io/cyanheads/obsidian-mcp-server:latest \
+  --push .
+
+bun run publish-mcp
+```
+
+---
+
 ## Imports
 
 ```ts
@@ -413,7 +451,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] If wrapping external API: tests include at least one sparse payload case with omitted upstream fields
 - [ ] Registered in `createApp()` arrays (directly or via barrel exports). Conditional registration (e.g. `commandToolDefinitions` behind `OBSIDIAN_ENABLE_COMMANDS`) happens in `src/index.ts`, not in the barrel
 - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
-- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
-- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
-- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name (never the npm scope — `lint:packaging` enforces this); `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; every user-supplied variable (API key, instance URL) is listed in `env_vars` so Codex forwards it from the user's environment. Never write `"KEY": ""` into `env` — an empty value replaces the user's exported key and is read as unset
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `author`, `repository`, `license`, `keywords` from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name. Every user-supplied variable is declared under `userConfig` (`type`, `title`, `description`; `sensitive: true` for keys and tokens; `required: true` or `default: ""`) and referenced from `env` as `"KEY": "${user_config.<option>}"` — mirror the `user_config` block in `manifest.json`. Never write `"KEY": ""` into `env`
 - [ ] `bun run devcheck` passes

package/Dockerfile

@@ -110,8 +110,9 @@ ENV MCP_HTTP_PORT=${PORT:-3010}
 # bind exposes the upstream OBSIDIAN_API_KEY to any caller that can reach the port.
 ENV MCP_HTTP_HOST="0.0.0.0"
 ENV MCP_TRANSPORT_TYPE="http"
-# Stateful because obsidian_delete_note confirms via ctx.requestInput; the
-# elicitation round backing that gate is disabled in stateless mode.
+# Stateful because obsidian_delete_note confirms via ctx.requestInput; under
+# stateless, a 2025-era HTTP client's confirmation round is refused by the
+# capability gate (client_capability_missing).
 ENV MCP_SESSION_MODE="stateful"
 ENV MCP_LOG_LEVEL="info"
 ENV LOGS_DIR="/var/log/obsidian-mcp-server"