oh-my-second-brain 0.2.0 → 0.3.0

package/adapters/claude-code/skills/uninstall/SKILL.md

@@ -1,34 +0,0 @@
----
-name: oms-uninstall
-description: Remove Oh My Second Brain host adapter and MCP registrations by running oms uninstall.
----
-
-# Skill: oms-uninstall (Claude Code)
-
-Remove Oh My Second Brain host registrations and adapter files. This does **not** delete vault notes or `vault/.oms/` ontology data.
-
-## Invocation
-
-```
-/oms-uninstall
-```
-
-## What this skill does
-
-Shells out to:
-
-```bash
-oms uninstall [--runtime <all|claude|codex|hermes>] [--dry-run] [--execute] [--yes]
-```
-
-## Recommended flow
-
-```bash
-# Preview first:
-oms uninstall --runtime all --dry-run
-
-# Remove Oh My Second Brain host registrations:
-oms uninstall --runtime all --yes
-```
-
-Use `--execute` only when you want Oh My Second Brain to call external host CLIs such as the scoped `claude mcp remove oms --scope local|project|user` commands or `claude plugin uninstall oms`.

package/adapters/claude-code/skills/update/SKILL.md

@@ -1,45 +0,0 @@
----
-name: oms-update
-description: Update Oh My Second Brain and refresh installed host adapters.
----
-
-# Skill: oms-update (Claude Code)
-
-Update the globally installed Oh My Second Brain package and reconcile host adapter surfaces.
-
-## Invocation
-
-```
-/oms-update
-```
-
-## What this skill does
-
-Shells out to:
-
-```bash
-oms update [--runtime <auto|all|claude|codex|hermes>] [--vault <path>] [--dry-run] [--yes]
-```
-
-The CLI will:
-1. Check the latest `oh-my-second-brain` version on npm.
-2. Print the planned package update and adapter reconciliation commands unless `--yes` is provided.
-3. With `--yes`, run `npm install -g oh-my-second-brain@latest`.
-4. Refresh host adapter/MCP registrations for the selected runtime.
-
-## Options
-
-| Flag | Description |
-|------|-------------|
-| `--vault <path>` | Vault path used for MCP registration refresh. |
-| `--runtime <name>` | Refresh `auto`, `all`, `claude`, `codex`, or `hermes`. |
-| `--dry-run` | Preview update and reconciliation commands without mutating anything. |
-| `--yes` | Perform the package update and adapter reconciliation. |
-| `--execute` | Allow external host CLIs during reconciliation where available. |
-
-## Example
-
-```bash
-oms update --dry-run --runtime all --vault ~/Documents/MyVault
-oms update --yes --runtime all --vault ~/Documents/MyVault
-```

package/adapters/claude-code/skills/vault-decision-record/SKILL.md

@@ -1,52 +0,0 @@
----
-name: oms-vault-decision-record
-description: Records vault structural changes as ADR markdown in .oms/governance/decisions/. Update rule is SUPERSEDE-ONLY — new ADRs supersede old ones; existing ADRs are never deleted.
----
-
-# Skill: oms-vault-decision-record (Claude Code)
-
-Record a vault structural decision as an Architecture Decision Record (ADR).
-
-## Invocation
-
-```
-/oms-vault-decision-record
-```
-
-## What this skill does
-
-Thin pointer to `core/skills/vault-decision-record`. Writes append-only ADR
-files to `vaultRoot/.oms/governance/decisions/`. History is permanent — ADRs
-are never deleted or renamed.
-
-## Agent-guided steps (v0)
-
-1. Scan `vaultRoot/.oms/governance/decisions/` for existing `ADR-NNNN-*.md` files
-   to determine the next sequential number. Create the directory if it does not exist.
-2. Slugify `title` (lowercase, hyphens, no special characters).
-3. Write `ADR-{NNNN}-{slug}.md` with the required frontmatter and three body sections:
-   **Context**, **Decision**, **Consequences**.
-4. If `supersedes` is provided, open the referenced ADR and set its `superseded_by`
-   field to the new ADR id. Never delete or rename the old file.
-5. Return `adrPath`, `adrId`, and `supersededPath` (or `null`).
-
-## Update rule — SUPERSEDE-ONLY
-
-- Never delete an existing ADR.
-- Never edit the `decision` or `consequences` body of an existing ADR.
-- To revise a decision, write a new ADR with `supersedes: ADR-{old}`.
-- `superseded_by` in the old ADR is the only mutation allowed on existing files.
-
-## Layer 1 CONTRACT guard
-
-Never read, write, or modify `core/ontology/taxonomy.yaml`,
-`core/ontology/concepts/*.yaml`, or `vaultRoot/.oms/taxonomy.yaml`.
-
-## Runtime
-
-No MCP tool required — this is a pure TypeScript call against the filesystem.
-
-## NOTES
-
-Wiki mirror deferred — the `wiki` skill is built by a parallel milestone (M3)
-and its adapter mirror is intentionally deferred until that milestone lands.

package/adapters/claude-code/skills/vault-lint/SKILL.md

@@ -1,47 +0,0 @@
----
-name: oms-vault-lint
-description: Checker-lane-only vault linter — enforces the Layer 1 CONTRACT (taxonomy.yaml + concepts/*.yaml) across all notes in a vault via five checks. Never mutates vault files.
----
-
-# Skill: oms-vault-lint (Claude Code)
-
-Verify that every markdown note in a vault conforms to its declared ontology.
-
-## Invocation
-
-```
-/oms-vault-lint
-```
-
-## What this skill does
-
-Thin pointer to `core/skills/vault-lint`. Runs five CONTRACT checks
-(allowlist, required, type, enum, routing-law) across all notes. Read-only by
-default; autofix requires explicit human-gate approval.
-
-## Agent-guided steps (v0)
-
-1. Load the ontology: `await loadOntology(path.join(vaultRoot, ".oms/ontology"))`.
-2. Call `lintVault(vaultRoot, ontology)`.
-3. If `report.clean` is false, surface `report.violations` to the user.
-   **Do NOT autofix without explicit user approval.**
-4. If autofix is explicitly approved, re-call with `{ autofixEnabled: true }`.
-   (Autofix is a no-op in v0.1.0 — reserved for a future human-gate protocol.)
-
-## Five checks
-
-1. **allowlist** — no frontmatter key outside the concept's declared field list.
-2. **required** — required fields must be present and non-empty.
-3. **type** — values must match the declared `FieldType` (string / url / date / list / number / boolean).
-4. **enum** — string fields with an `enum` array must use a listed value.
-5. **routing-law** — notes in agent-writable taxonomy zones must carry `created_by`.
-
-## Runtime
-
-`lintVault` returns a `VaultLintReport`: `violations`, `scannedNotes`, `clean`.
-No MCP tool is required — this is a pure TypeScript call against the filesystem.
-
-## NOTES
-
-Wiki mirror deferred — the `wiki` skill is built by a parallel milestone (M3)
-and its adapter mirror is intentionally deferred until that milestone lands.

package/adapters/claude-code/skills/vault-scaffold/SKILL.md

@@ -1,47 +0,0 @@
----
-name: oms-vault-scaffold
-description: Seeds a vault with the default taxonomy, creates a decisions/ zone, writes governance stubs, and records the per-vault .oms/taxonomy.yaml override path. All writes are additive — existing files are never overwritten.
----
-
-# Skill: oms-vault-scaffold (Claude Code)
-
-Seed a fresh vault with the standard OMS folder structure and governance stubs.
-
-## Invocation
-
-```
-/oms-vault-scaffold
-```
-
-## What this skill does
-
-Thin pointer to `core/skills/vault-scaffold`. Safe to re-run on an existing
-vault — all writes are additive; existing files are never overwritten.
-
-## Agent-guided steps (v0)
-
-1. Read `core/ontology/taxonomy.yaml` to load the engine DEFAULT folder→concept map.
-2. For each folder declared in `taxonomy.yaml`, create the directory under `vaultRoot`
-   if it does not already exist.
-3. Create `vaultRoot/decisions/` for human-authored structural decision records.
-4. Write `vaultRoot/.oms/taxonomy.yaml` as the per-vault override path
-   (initial content is a verbatim copy of the engine DEFAULT).
-5. Write `vaultRoot/.oms/governance/architecture.md` stub.
-6. Return the scaffold report: `created`, `skipped`, and `taxonomyZones`.
-
-## Constraints
-
-- Never writes outside `vaultRoot`.
-- Never modifies `core/ontology/taxonomy.yaml` or `core/ontology/concepts/*.yaml`
-  (Layer 1 CONTRACT files — read-only from this skill).
-- `mkdir -p` semantics — missing intermediate directories are created.
-
-## Runtime
-
-No MCP tool required — this is a pure TypeScript call against the filesystem.
-Use `overwrite: false` (default) to preserve existing files on subsequent runs.
-
-## NOTES
-
-Wiki mirror deferred — the `wiki` skill is built by a parallel milestone (M3)
-and its adapter mirror is intentionally deferred until that milestone lands.

package/adapters/claude-code/skills/wiki/SKILL.md

@@ -1,82 +0,0 @@
----
-name: oms-wiki
-description: Two-path wiki skill — Path A: promote compiled concepts from processed/ into the wiki/ query surface; Path B (human authoring): build interlinked terminology notes in vault taxonomy folders via write.
----
-
-# Skill: oms-wiki (Claude Code)
-
-Two-path skill — thin pointer to `core/skills/wiki`. Requires `OMS_VAULT`.
-
-## Invocation
-
-```
-/wiki
-```
-
-## Which path?
-
-Check **before acting**:
-- **Path A:** you have compiled `processed/<concept>.md` output → promote into `wiki/`.
-- **Path B (human authoring):** you have only a topic + terms, no compile output → use MCP `write`, writes to vault taxonomy folders.
-
-These paths are **mutually exclusive**.
-
----
-
-## Path A — promotion
-
-*(Only when `processed/<concept>.md` exists.)*
-
-### Agent-guided steps
-
-1. Verify `processed/<concept>.md` exists.
-2. Load the staleness ledger from `.llmwiki/staleness.json`.
-3. Promote `processed/→wiki/`, update the ledger, flip cascade backlinks,
-   and detect stubs and orphans.
-4. Regenerate `wiki/index.md` and append an entry to `wiki/log.md`.
-5. Lint — auto-fix index consistency, broken `[[wikilinks]]`, and See-Also
-   sections; report conflicts, orphans, and outdated refs.
-
-### Staleness states
-
-| State | Meaning |
-|-------|---------|
-| `CLEAN` | Compile output matches current sources |
-| `DIRTY` | Source SHA changed; needs recompile |
-| `STUB` | Referenced by wikilinks but no compile output exists |
-| `ORPHAN` | No incoming wikilinks from any other wiki page |
-| `CONFLICT` | Two compile sources produced conflicting content |
-
-Full-rebuild escape hatch: delete `.llmwiki/staleness.json` — every page resets to DIRTY.
-
-`processed/` is internal — NEVER synced to the Obsidian vault.
-A wiki run never triggers compile; compile never writes `wiki/` directly.
-
----
-
-## Path B — Human authoring
-
-*(Only when no compiled `processed/` output exists.)*
-
-Build a hub/MOC note plus one standalone note per coined term, cross-linked with
-`[[wikilinks]]` and committed via MCP `write`.
-Writes to vault taxonomy folders — **never to `wiki/`**.
-
-### Admission gate
-
-Apply before any MCP `write` call:
-- **Coined/proper term** (only ever means one specific technical thing) → standalone note.
-- **General noun** (meaning shifts by domain) → `## Term` section inside the hub note.
-
-K8s example: `Pod`, `Service`, `Deployment`, `Ingress` → hub sections;
-`ReplicaSet`, `StatefulSet`, `DaemonSet`, `CronJob` → standalone notes.
-
-### Agent-guided steps
-
-1. Ask for the **topic** and **term list**.
-2. Resolve the **target concept/folder** from `vault/.oms/taxonomy.yaml`.
-3. Apply the admission gate to every term.
-4. **Deduplicate**: MCP `write` `mode: "create"` per coined term; if the note already exists, reuse the `[[wikilink]]`.
-5. Draft coined-term notes (definition + `## See Also` back-link to hub). Commit terms first.
-6. Draft hub/MOC note (general-noun `## Term` sections + `## See Also` coined-term links). Commit hub last.
-7. Run `oms doctor` (non-blocking, exits 0).

package/adapters/claude-code/skills/write/SKILL.md

@@ -1,16 +0,0 @@
----
-name: oms-write
-description: Write a vault note through the Oh My Second Brain kernel contract.
----
-
-# Skill: oms-write (Claude Code)
-
-## Invocation
-
-```
-/oms-write
-```
-
-Call MCP `write`. Do not use host Write/Edit for vault `.md` files.
-
-`mode` is `create`, `append`, or `update`. The kernel owns `.oms` and returns `ask`, `inbox`, `written`, or `rejected`.

package/adapters/codex/skills/oms-compile/SKILL.md

@@ -1,16 +0,0 @@
----
-name: oms-compile
-description: Agent-guided concept compile — synthesize a concept wiki page from source materials with incremental skip, provenance weighting, and cascade backlinks.
----
-
-# oms-compile
-
-Thin pointer to `core/skills/compile`. There is no `oms compile` CLI. Two phases:
-
-1. **Phase A** — load and grade source materials (pure read). Resolve backlinks.
-2. **Phase B** — write synthesized `body` to `processed/` only; never to `wiki/`.
-
-Skip Phase B if the material SHA is unchanged.
-Pass affected backlinks to the wiki skill to mark stale pages.
-Provenance order: authored > curated > external-raw.
-Delete `{dotLlmwiki}/sha-cache.json` to force a full recompile.

package/adapters/codex/skills/oms-distill/SKILL.md

@@ -1,14 +0,0 @@
----
-name: oms-distill
-description: Standalone meta-absorption skill — analyzes any target in a clean-room context and produces a structured absorption report with patterns, risks, and attribution. Vault-agnostic.
----
-
-# oms-distill
-
-Thin pointer to `core/skills/distill`. Vault-agnostic — `OMS_VAULT` not required.
-
-1. Load the target as inert read-only text; never execute it.
-2. Snapshot a content hash before analysis. Run a read-only red-team pass.
-3. Write the report: §1 Patterns, §2 Risks, §3 Attribution.
-4. Verify the hash is unchanged. Stop if anything mutated.
-5. Return the report string. No vault write occurs inside distill.

package/adapters/codex/skills/oms-doctor/SKILL.md

@@ -1,14 +0,0 @@
----
-name: oms-doctor
-description: Validate vault notes against the active Oh My Second Brain ontology.
----
-
-# oms-doctor
-
-Run:
-
-```bash
-oms doctor --vault <vault>
-```
-
-The command is advisory in v0 and exits 0 even when warnings are found.

package/adapters/codex/skills/oms-install/SKILL.md

@@ -1,19 +0,0 @@
----
-name: oms-install
-description: Install Oh My Second Brain Codex/Hermes/Claude host adapters and MCP registration.
----
-
-# oms-install
-
-Use for host lifecycle installation.
-
-```bash
-oms install --runtime <auto|all|claude|codex|hermes> --vault <vault> --yes
-```
-
-For Codex, this installs:
-
-- `~/.codex/rules/oms.md`
-- `~/.codex/skills/oms-*`
-- `~/.codex/plugins/oms`
-- managed `[mcp_servers.oms]` in `~/.codex/config.toml`

package/adapters/codex/skills/oms-link/SKILL.md

@@ -1,35 +0,0 @@
----
-name: oms-link
-description: Two-path note-linking skill — Path A (pre-write): compose a new note body that already carries [[wikilinks]] to existing term notes; Path B (retrofit): add missing links to existing notes via oms linkify or oms_link_apply.
----
-
-# oms-link
-
-Thin pointer to `core/skills/link`. Requires `OMS_VAULT`.
-
-Determine which path applies before acting. These paths are **mutually exclusive**.
-
-Link targets are ONLY notes bound to the `term` concept in `vault/.oms/taxonomy.yaml`; their surface forms are the basename and the frontmatter `aliases`. Three engine rules hold in both paths: a link exists only where the term literally appears (surface-anchored, never invented by retrieval); first occurrence per target note only; ambiguity (`ambiguous: true` + `rivalPaths`) is reported and never auto-resolved — ask the user or skip the span. Frontmatter, code, existing links, headings, URLs, and tags are masked out, so a "missing" link inside any of them is correct.
-
-## Path A — pre-write linking
-
-*(Use while drafting, so the note lands already linked and needs no retrofit.)*
-
-1. Call MCP `oms_link_suggest` on an existing note in the same folder (or run `oms linkify --folder <folder>` in report mode) and read the `targetPath` list — that is the vault's current term vocabulary.
-2. Draft the body with those exact surface forms, writing `[[wikilinks]]` inline at the first mention of each term.
-3. Commit via MCP `write`. Host file edits never touch vault `.md`.
-4. Re-check with `oms_link_suggest`: zero candidates means the draft was already fully linked.
-
-NOTE: `0 term note(s) available as link targets` means the vault has no term layer yet — build one with the `oms-wiki` skill first.
-
-## Path B — retrofit existing notes
-
-*(Use when the note is already on disk. Report first, always.)*
-
-1. `oms linkify --folder <folder>` — report only, writes nothing.
-2. Show the report and get agreement before mutating anything.
-3. Whole folder → `oms linkify --folder <folder> --apply --yes`. `--apply` without `--yes` refuses before reading any note and writes nothing.
-4. Per-note acceptance → `oms_link_suggest { notePath, folder? }` returns candidates plus `baseContentHash`; drop unresolved ambiguous ones; then `oms_link_apply { notePath, baseContentHash, candidateIds, folder? }` with the SAME `baseContentHash` and the SAME `folder` scope.
-5. Run `oms doctor` after a retrofit run (non-blocking, exits 0).
-
-NOTE: `oms_link_apply` refuses without writing on `note-changed`, `candidate-drift`, or overlapping candidates. Re-run `oms_link_suggest` for fresh offsets instead of retrying stale ids. Every write — CLI or MCP — goes through the capture kernel, so path safety and the concept contract hold.

package/adapters/codex/skills/oms-retrieve/SKILL.md

@@ -1,32 +0,0 @@
----
-name: oms-retrieve
-description: Retrieve vault knowledge axis-first using folders, frontmatter, wikilinks, and declared lenses.
----
-
-# oms-retrieve
-
-Use `oms_retrieve_context` first for natural-language retrieval. It combines live
-frontmatter/folder/wikilink graph context with optional OMS native semantic
-lexical/SQLite-vector/HYDE candidates and does not require a warm graph cache. Pass declared
-concept/folder/property/value/wikilink axes when the user's intent gives them.
-
-Use `semanticScope: "global"` for broad vault-wide semantic search. Use
-`semanticScope: "graph"` (**gph mode**) when semantic candidates must stay inside
-the selected OMS graph candidates.
-
-Pass typed sub-queries via `semanticSearches` to combine search strategies in one call:
-`type: "lex"` for BM25 keyword search, `type: "vec"` for SQLite-vector semantic
-search, and `type: "hyde"` for hypothetical-document expansion. Pass `semanticMode`,
-`semanticIntent`, `semanticLex`, `semanticVec`, `semanticHyde`, and
-`semanticMinScore` for additional typed or thresholded control. Pass
-`embeddingSyncBeforeSearch: true` when the native semantic index must be refreshed
-before retrieval, or call `oms_sync_embeddings` explicitly.
-Use read-only `oms_get_document` or `oms_multi_get_documents` to rehydrate selected
-docids, paths, globs, or line ranges. Use `oms_semantic_query`,
-`oms_semantic_status`, `oms_semantic_collections`, or `oms_semantic_contexts` for
-qmd-compatible follow-ups on the native OMS index.
-
-Use `oms_retrieve_by_axis` only for legacy axis-first cache retrieval. Use
-`oms_lazy_load_note` only after selecting candidate notes.
-
-Return lens-shaped fields where possible; do not dump full note bodies unless the user asks or the retrieval task needs body evidence.

package/adapters/codex/skills/oms-setup/SKILL.md

@@ -1,34 +0,0 @@
----
-name: oms-setup
-description: Adopt an Obsidian markdown vault into the Oh My Second Brain convention and optionally install host MCP integration.
----
-
-# oms-setup
-
-Use when the user wants to initialize Oh My Second Brain for a vault.
-
-Run:
-
-```bash
-oms setup --vault <vault>
-```
-
-For a non-interactive first pass:
-
-```bash
-oms setup --vault <vault> --yes
-```
-
-To interview each folder axis and merge observed note frontmatter into concept schemas:
-
-```bash
-oms setup --vault <vault> --suggest-fields
-```
-
-Then, when host registration is desired:
-
-```bash
-oms install --runtime codex --vault <vault> --yes
-```
-
-Setup interviews folder intent, concept binding, optional observed fields, and retrieval lenses. It rejects lenses that reference unknown fields. Do not modify vault notes during setup. Oh My Second Brain writes only `vault/.oms/taxonomy.yaml` and `vault/.oms/concepts/`, preserving existing concept files while adding missing defaults or selected observed fields.

package/adapters/codex/skills/oms-uninstall/SKILL.md

@@ -1,20 +0,0 @@
----
-name: oms-uninstall
-description: Remove Oh My Second Brain host adapter files and MCP registration without deleting vault notes or vault ontology.
----
-
-# oms-uninstall
-
-Preview first:
-
-```bash
-oms uninstall --runtime all --dry-run
-```
-
-Remove host registrations:
-
-```bash
-oms uninstall --runtime all --yes
-```
-
-Never delete vault notes or `vault/.oms/` as part of host uninstall.

package/adapters/codex/skills/oms-update/SKILL.md

@@ -1,22 +0,0 @@
----
-name: oms-update
-description: Update Oh My Second Brain and refresh installed host adapter registrations.
----
-
-# oms-update
-
-Use when the user wants to update Oh My Second Brain after it has already been installed.
-
-Preview first:
-
-```bash
-oms update --dry-run --runtime all --vault <vault>
-```
-
-Perform the update:
-
-```bash
-oms update --yes --runtime all --vault <vault>
-```
-
-`oms update` checks npm for the latest `oh-my-second-brain` release, installs `oh-my-second-brain@latest` only when `--yes` is present, then reconciles host adapter/MCP registrations through the same install path. Without `--yes`, it prints the planned commands and does not mutate package or host config.

package/adapters/codex/skills/oms-vault-lint/SKILL.md

@@ -1,19 +0,0 @@
----
-name: oms-vault-lint
-description: Checker-lane-only vault linter — enforces the Layer 1 CONTRACT (taxonomy.yaml + concepts/*.yaml) via five checks. Never mutates vault files.
----
-
-# oms-vault-lint
-
-Thin pointer to `core/skills/vault-lint`. Read-only by default.
-
-Rules:
-
-1. Load ontology: `await loadOntology(path.join(vaultRoot, ".oms/ontology"))`.
-2. Call `lintVault(vaultRoot, ontology)`.
-3. Surface `report.violations` to the user if `report.clean` is false. Do NOT autofix without explicit approval.
-4. Re-call with `{ autofixEnabled: true }` only after explicit user confirmation (no-op in v0.1.0).
-
-Five checks: allowlist, required, type, enum, routing-law.
-
-NOTE: Wiki mirror deferred — depends on M3.

package/adapters/codex/skills/oms-wiki/SKILL.md

@@ -1,39 +0,0 @@
----
-name: oms-wiki
-description: Two-path wiki skill — Path A: promote compiled concepts from processed/ into the wiki/ query surface; Path B (human authoring): build interlinked terminology notes in vault taxonomy folders via write.
----
-
-# oms-wiki
-
-Thin pointer to `core/skills/wiki`. Requires `OMS_VAULT`.
-
-Determine which path applies before acting. These paths are **mutually exclusive**.
-
-## Path A — promotion
-
-*(Use only when `processed/<concept>.md` already exists.)*
-
-1. Verify `processed/<concept>.md` exists.
-2. Load staleness ledger from `.llmwiki/staleness.json`.
-3. Promote `processed/→wiki/`, update ledger, flip cascade backlinks, detect stubs and orphans.
-4. Regenerate `wiki/index.md` and append to `wiki/log.md`.
-5. Lint: auto-fix (index consistency, broken links, See-Also) and report-only (conflicts, orphans, outdated refs).
-
-NOTE: `processed/` is internal — never synced to the Obsidian vault. Only `wiki/` crosses the sync boundary.
-
-## Path B — Human authoring
-
-*(Use when you have only a topic + terms and no compiled `processed/` output.)*
-
-1. Ask the user for a **topic** and **term list** (or extract terms from freeform source text).
-2. Resolve the **target concept/folder** from `vault/.oms/taxonomy.yaml`.
-3. Apply the **admission gate** to every term:
-   - Coined/proper term (only ever means one specific technical thing) → standalone note.
-   - General noun (meaning shifts by domain) → `## Term` section inside the hub note only.
-   - K8s example: `Pod`, `Service`, `Deployment`, `Ingress` → hub sections; `ReplicaSet`, `StatefulSet`, `DaemonSet`, `CronJob` → standalone notes.
-4. **Deduplicate**: call MCP `write` with `mode: "create"` for each coined term; if the note already exists, reuse the `[[wikilink]]`.
-5. Draft coined-term notes: frontmatter from the concept's required fields + definition + `## See Also` back-link to the hub. Commit terms first via MCP `write`.
-6. Draft hub/MOC note: general-noun `## Term` sections + `## See Also` listing all coined-term `[[wikilinks]]`. Commit hub last via MCP `write`.
-7. Run `oms doctor` after all notes are committed (non-blocking, exits 0).
-
-NOTE: Path B writes to vault taxonomy folders — **never to `wiki/`**.

package/adapters/codex/skills/oms-write/SKILL.md

@@ -1,10 +0,0 @@
----
-name: oms-write
-description: Write a vault note through the Oh My Second Brain kernel contract.
----
-
-# oms-write
-
-Call MCP `write`. Do not use host Write/Edit for vault `.md` files.
-
-`mode` is `create`, `append`, or `update`. The kernel owns `.oms` and returns `ask`, `inbox`, `written`, or `rejected`.

package/adapters/hermes/skills/compile/SKILL.md

@@ -1,13 +0,0 @@
----
-name: compile
-description: Agent-guided concept compile — synthesize a concept wiki page from source materials with incremental skip, provenance weighting, and cascade backlinks.
----
-
-# oms-compile
-
-Thin pointer to `core/skills/compile`. There is no `oms compile` CLI.
-
-Phase A — load and grade source materials (pure read). Resolve backlinks.
-Phase B — write synthesized body to `processed/` only; never to `wiki/`.
-
-Skip Phase B if the material SHA is unchanged. Pass affected backlinks to the wiki skill. Provenance order: authored > curated > external-raw. Delete `{dotLlmwiki}/sha-cache.json` to force a full recompile.

package/adapters/hermes/skills/distill/SKILL.md

@@ -1,10 +0,0 @@
----
-name: distill
-description: Standalone meta-absorption skill — analyzes any target in a clean-room context and produces a structured absorption report with patterns, risks, and attribution. Vault-agnostic.
----
-
-# oms-distill
-
-Thin pointer to `core/skills/distill`. Vault-agnostic — `OMS_VAULT` not required.
-
-Load the target as inert text only, never execute. Snapshot a content hash, run a read-only red-team pass, then write §1 Patterns, §2 Risks, §3 Attribution. Verify the hash is unchanged. Return the report string — no vault write occurs inside distill.

package/adapters/hermes/skills/doctor/SKILL.md

@@ -1,14 +0,0 @@
----
-name: doctor
-description: Validate vault notes against the active Oh My Second Brain ontology.
----
-
-# oms-doctor
-
-Run:
-
-```bash
-oms doctor --vault <vault>
-```
-
-The command is advisory in v0 and exits 0 even when warnings are found.