oh-my-second-brain 0.2.0 → 0.3.0

package/assets/skills/doctor/SKILL.md

@@ -0,0 +1,23 @@
+---
+name: doctor
+description: Diagnose vault convention and index problems, then run explicit repairs.
+mcp_tool: oms_doctor
+mcp_args:
+  op: "audit"
+---
+
+# doctor
+
+Diagnose vault problems and perform the requested repair.
+
+## Use when
+
+Use this skill when a vault has convention violations, an unhealthy graph or semantic index, or stale generated state that needs correction. Use `status` instead when inspection alone is required.
+
+## Usage
+
+```text
+/doctor <audit|validate|build-graph|semantic-cleanup|sync-embeddings>
+```
+
+`audit` and `validate` inspect notes against their declared concept schemas. `build-graph`, `semantic-cleanup`, and `sync-embeddings` are repair operations and may write generated graph or semantic-index state. Review the diagnosis, then invoke only the repair needed.

package/assets/skills/link/SKILL.md

@@ -0,0 +1,24 @@
+---
+name: link
+description: Suggest or apply safe wikilinks between vault notes.
+mcp_tool: oms_link
+mcp_args:
+  op: "suggest"
+  notePath: "$1"
+---
+
+# link
+
+Suggest or apply `[[wikilinks]]` between a note and the vault's term notes.
+
+## Use when
+
+Use `suggest` before writing or revising a note, or use `apply` to add accepted links to an existing note.
+
+## Usage
+
+```text
+/link <suggest|apply> <vault-relative-note-path>
+```
+
+Link targets are term notes only. Suggestions are surface-anchored, add at most one link per target in a body, and report ambiguous matches rather than resolving them. Applying suggestions writes through the vault write kernel and requires the suggestion's `baseContentHash` and accepted candidate IDs.

package/assets/skills/search/SKILL.md

@@ -0,0 +1,25 @@
+---
+name: search
+description: Retrieve vault knowledge through declared retrieval lenses.
+aliases: [retrieve]
+mcp_tool: oms_search
+mcp_args:
+  op: "semantic-query"
+  query: "$1"
+---
+
+# search
+
+Retrieve notes and declared fields for a vault question. A lens is a vault-declared retrieval view, not an ad-hoc query filter: it identifies which fields matter for a purpose such as synthesis or audit.
+
+## Use when
+
+Use this skill to find and assemble relevant vault knowledge without changing the vault.
+
+## Usage
+
+```text
+/search <query>
+```
+
+Choose the declared lens that matches the request, return only that lens's fields, and group results by concept or folder. Search may combine the live note, frontmatter, and wikilink graph with available semantic candidates; graph results remain available when the semantic index is unavailable.

package/assets/skills/status/SKILL.md

@@ -0,0 +1,22 @@
+---
+name: status
+description: Report read-only vault health, statistics, and index state.
+mcp_tool: oms_status
+mcp_args: {}
+---
+
+# status
+
+Report the current state of a vault without changing it.
+
+## Use when
+
+Use this skill to inspect vault health and statistics before deciding whether maintenance is needed.
+
+## Usage
+
+```text
+/status
+```
+
+Report note counts, semantic-index availability and freshness, and graph-cache status. Status is observational only: it never rebuilds an index, repairs notes, or writes vault files.

package/assets/skills/write/SKILL.md

@@ -0,0 +1,30 @@
+---
+name: write
+description: Write a vault note through the Oh My Second Brain kernel contract.
+mcp_tool: oms_write
+mcp_args:
+  op: "create"
+  notePath: "$1"
+  body: "$2"
+---
+
+# write
+
+Write, append to, or update a vault note through MCP `oms_write`. Do not use host Write/Edit for vault `.md` files.
+
+## Use when
+
+Use this skill for every vault-note mutation.
+
+## Usage
+
+```text
+/write <create|append|update> <vault-relative-note-path> [body]
+```
+
+Use `op` with `create`, `append`, or `update`. The kernel owns `.oms` and returns one status:
+
+- `ask` — fill the missing or invalid fields and call `write` again
+- `inbox` — tell the user; do not invent a folder
+- `written` — done
+- `rejected` — fix `violations` or `reason` and call `write` again

package/core/ontology/schemas/README.md

@@ -1,14 +1,20 @@
-# core/ontology/schemas/
+# Schema reference assets
 
-Layer 1 CONTRACT — frontmatter schema definitions for all vault note types.
+The `*.schema.yaml` files in this directory are shipped reference assets. They
+are not installed into a vault and are not read by the current setup workflow.
 
-## What lives here
+## Setup output
 
-Each `*.schema.yaml` file declares the allowed frontmatter fields, types, enums,
-and required flags for one note type. These files are the authoring source;
-at vault setup time, `vault-scaffold` copies them into the vault's own `.oms/schemas/`.
+`oms setup` creates the vault's `.oms/` directory and writes:
 
-## Current schemas
+- `.oms/taxonomy.yaml`, containing the configured folder-to-concept bindings.
+- `.oms/concepts/`, containing bundled concept documents from
+  `core/ontology/concepts/` when a document does not already exist locally.
+
+Setup does not create `.oms/schemas/` or copy files from this directory. The
+live convention model is the taxonomy plus concept documents above.
+
+## Reference files
 
 | File | Note type | Key constraint |
 |------|-----------|----------------|
@@ -31,19 +37,19 @@ fields:
     enum: [...]        # only when type: enum
     normalize: kebab   # optional — normalize list values to kebab-case
 
-lenses:                # optional — named retrieval views (see retrieve skill)
+lenses:                # optional named retrieval views
   - name: <lens>
     intent: "..."
     fields: [...]
 
 validation:
   allow_extra_fields: true   # vault notes may carry additional ad-hoc keys
-  strict_enum: true          # enum violations are hard errors in vault-lint
+  strict_enum: true          # enum violations are hard errors
 ```
 
-## Invariants (ADR-006 Layer 1)
+## Reference constraints
 
-- These files are parsed by `vault-lint` and `oms_validate_contract`. No prose rationale.
-- Rationale for *why* a field exists belongs in `.oms/governance/` (Layer 2), not here.
-- Adding a required field is a breaking change — all existing notes must be migrated first.
-- `allow_extra_fields: true` is the default; vault notes routinely carry personal ad-hoc keys.
+- Changes to these reference files do not change a configured vault.
+- The active fields and constraints for a vault live in its `.oms/concepts/`
+  documents.
+- Adding a required field to an active concept requires updating existing notes.

package/dist/assets/shared-skills.d.ts

@@ -0,0 +1,4 @@
+/** The single authored skill source used by every host installer. */
+export declare const SHARED_SKILLS_SOURCE = "assets/skills";
+/** Absolute path to the shared skill source beneath `packageRoot`. */
+export declare function resolveSharedSkillsSource(packageRoot: string): string;

package/dist/assets/shared-skills.js

@@ -0,0 +1,8 @@
+import path from "node:path";
+/** The single authored skill source used by every host installer. */
+export const SHARED_SKILLS_SOURCE = "assets/skills";
+/** Absolute path to the shared skill source beneath `packageRoot`. */
+export function resolveSharedSkillsSource(packageRoot) {
+    return path.join(packageRoot, ...SHARED_SKILLS_SOURCE.split("/"));
+}
+//# sourceMappingURL=shared-skills.js.map

package/dist/assets/shared-skills.js.map

@@ -0,0 +1 @@
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package/dist/cli/args.d.ts

@@ -1,4 +1,4 @@
-import type { RuntimeSelection } from "../install/hosts.js";
+import type { RuntimeSelection } from "../kernel/install/hosts.js";
 export declare class CliArgumentError extends Error {
     constructor(message: string);
 }

package/dist/cli/args.js

@@ -1,5 +1,5 @@
 import path from "node:path";
-import { harnessSurfaceRegistry } from "../harness/surface-registry.js";
+import { harnessSurfaceRegistry } from "../kernel/harness/surface-registry.js";
 export class CliArgumentError extends Error {
     constructor(message) {
         super(message);

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package/dist/cli/audit.js

@@ -1,6 +1,6 @@
-import { collectObservedFields, collectObservedFieldValues, } from "../setup/axis.js";
-import { lintVault } from "../engine/conventions/vault-lint.js";
-import { resolveActiveOntology } from "../ontology/active.js";
+import { collectObservedFields, collectObservedFieldValues, } from "../kernel/setup/axis.js";
+import { lintVault } from "../kernel/engine/conventions/vault-lint.js";
+import { resolveActiveOntology } from "../kernel/ontology/active.js";
 /** Fields observed in a folder that its bound concept(s) do not declare. */
 function undeclaredObservedFields(ontology, summary) {
     const binding = ontology.taxonomy.folders[summary.folder];

package/dist/cli/audit.js.map

@@ -1 +1 @@
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+{"version":3,"file":"audit.js","sourceRoot":"","sources":["../../src/cli/audit.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,qBAAqB,EACrB,0BAA0B,GAG3B,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,SAAS,EAA2B,MAAM,4CAA4C,CAAC;AAChG,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAGrE,4EAA4E;AAC5E,SAAS,wBAAwB,CAC/B,QAAkB,EAClB,OAA+E;IAE/E,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;IAC1D,IAAI,CAAC,OAAO,IAAI,OAAO,CAAC,OAAO,KAAK,IAAI;QAAE,OAAO,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;IACrE,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;IAC1F,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAU,CAAC;IACnC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE,CAAC;QAChC,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC5C,IAAI,CAAC,OAAO;YAAE,SAAS;QACvB,KAAK,MAAM,KAAK,IAAI,OAAO,CAAC,MAAM;YAAE,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;IAC/D,CAAC;IACD,OAAO,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;AACrE,CAAC;AAGD,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,IAK9B;IACC,MAAM,EAAE,KAAK,EAAE,IAAI,GAAG,KAAK,EAAE,MAAM,EAAE,aAAa,GAAG,KAAK,EAAE,GAAG,IAAI,CAAC;IAEpE,IAAI,CAAC;QACH,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,qBAAqB,CAAC,KAAK,CAAC,CAAC;QACxD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,KAAK,EAAE,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;QAE5D,IAAI,eAAe,GAAuD,EAAE,CAAC;QAC7E,IAAI,WAAW,GAAuC,EAAE,CAAC;QACzD,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,QAAQ,GAAG,MAAM,qBAAqB,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;YAC1E,eAAe,GAAG,QAAQ;iBACvB,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;gBACjB,MAAM,EAAE,OAAO,CAAC,MAAM;gBACtB,MAAM,EAAE,wBAAwB,CAAC,QAAQ,EAAE,OAAO,CAAC;aACpD,CAAC,CAAC;iBACF,MAAM,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;YAClD,WAAW,GAAG,MAAM,0BAA0B,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;QAC9E,CAAC;QAED,IAAI,IAAI,EAAE,CAAC;YACT,OAAO,CAAC,GAAG,CACT,IAAI,CAAC,SAAS,CACZ;gBACE,KAAK;gBACL,MAAM,EAAE,MAAM,IAAI,IAAI;gBACtB,YAAY,EAAE,MAAM,CAAC,YAAY;gBACjC,aAAa,EAAE,MAAM,CAAC,aAAa;gBACnC,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,UAAU,EAAE,MAAM,CAAC,UAAU;gBAC7B,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,eAAe,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAC3D,EACD,IAAI,EACJ,CAAC,CACF,CACF,CAAC;QACJ,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CACT,+BAA+B,MAAM,CAAC,YAAY,qBAAqB,MAAM,CAAC,aAAa,cAAc,MAAM,CAAC,UAAU,CAAC,MAAM,gBAAgB,CAClJ,CAAC;YAEF,IAAI,MAAM,CAAC,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACnC,OAAO,CAAC,GAAG,CAAC,kDAAkD,CAAC,CAAC;YAClE,CAAC;iBAAM,CAAC;gBACN,MAAM,MAAM,GAAG,IAAI,GAAG,EAAgC,CAAC;gBACvD,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;oBAC1C,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;oBAClD,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;oBACrB,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC;gBACvC,CAAC;gBACD,KAAK,MAAM,CAAC,QAAQ,EAAE,UAAU,CAAC,IAAI,MAAM,EAAE,CAAC;oBAC5C,OAAO,CAAC,GAAG,CAAC,OAAO,QAAQ,EAAE,CAAC,CAAC;oBAC/B,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;wBACnC,OAAO,CAAC,GAAG,CAAC,QAAQ,SAAS,CAAC,IAAI,KAAK,SAAS,CAAC,OAAO,EAAE,CAAC,CAAC;oBAC9D,CAAC;gBACH,CAAC;gBACD,OAAO,CAAC,GAAG,CAAC,KAAK,MAAM,CAAC,UAAU,CAAC,MAAM,wBAAwB,MAAM,CAAC,IAAI,aAAa,CAAC,CAAC;YAC7F,CAAC;YAED,IAAI,aAAa,EAAE,CAAC;gBAClB,OAAO,CAAC,GAAG,CAAC,+EAA+E,CAAC,CAAC;gBAC7F,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC;oBAAE,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;gBAC1D,KAAK,MAAM,OAAO,IAAI,eAAe,EAAE,CAAC;oBACtC,MAAM,SAAS,GAAG,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,IAAI,KAAK,CAAC,IAAI,IAAI,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBAC1G,OAAO,CAAC,GAAG,CAAC,KAAK,OAAO,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC,CAAC;gBACnD,CAAC;gBAED,OAAO,CAAC,GAAG,CAAC,0EAA0E,CAAC,CAAC;gBACxF,MAAM,GAAG,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACrC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;oBAAE,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;gBAC9C,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;oBACxB,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,MAAM,MAAM,KAAK,CAAC,KAAK,OAAO,KAAK,CAAC,KAAK,MAAM,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;gBACxF,CAAC;gBACD,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;YAClB,CAAC;QACH,CAAC;QAED,OAAO,MAAM,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC9C,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,mCAAmC,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC3G,OAAO,CAAC,CAAC;IACX,CAAC;AACH,CAAC"}

package/dist/cli/claude-install-plan.js

@@ -1,4 +1,4 @@
-import { resolveBundledAssetPaths } from "../core/runtime/assets.js";
+import { resolveBundledAssetPaths } from "../kernel/runtime/assets.js";
 const bundledAssets = resolveBundledAssetPaths();
 function shellQuote(value) {
     if (/^[A-Za-z0-9_/:=.,@%+-]+$/.test(value)) {
@@ -7,7 +7,7 @@ function shellQuote(value) {
     return `'${value.replace(/'/g, "'\\''")}'`;
 }
 export function buildClaudeInstallPlan(_opts) {
-    const pluginPath = bundledAssets.claudeAdapterDir;
+    const pluginPath = bundledAssets.packageRoot;
     return {
         pluginPath,
         pluginInstallCommand: `claude plugin install ${shellQuote(pluginPath)}`,

package/dist/cli/claude-install-plan.js.map

@@ -1 +1 @@
-{"version":3,"file":"claude-install-plan.js","sourceRoot":"","sources":["../../src/cli/claude-install-plan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,wBAAwB,EAAE,MAAM,2BAA2B,CAAC;AAErE,MAAM,aAAa,GAAG,wBAAwB,EAAE,CAAC;AASjD,SAAS,UAAU,CAAC,KAAa;IAC/B,IAAI,0BAA0B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3C,OAAO,KAAK,CAAC;IACf,CAAC;IACD,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC;AAC7C,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAwB;IAC7D,MAAM,UAAU,GAAG,aAAa,CAAC,gBAAgB,CAAC;IAClD,OAAO;QACL,UAAU;QACV,oBAAoB,EAAE,yBAAyB,UAAU,CAAC,UAAU,CAAC,EAAE;QACvE,cAAc,EAAE,GAAG,UAAU,YAAY;QACzC,gBAAgB,EAAE,qBAAqB;KACxC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,IAAuB;IAC5D,OAAO,CAAC,GAAG,CAAC,6CAA6C,CAAC,CAAC;IAC3D,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IACjD,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,CAAC,oBAAoB,EAAE,CAAC,CAAC;IAC9D,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IACnD,OAAO,CAAC,GAAG,CAAC,8FAA8F,CAAC,CAAC;IAC5G,OAAO,CAAC,GAAG,CACT,oHAAoH,CACrH,CAAC;AACJ,CAAC"}
+{"version":3,"file":"claude-install-plan.js","sourceRoot":"","sources":["../../src/cli/claude-install-plan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AAEvE,MAAM,aAAa,GAAG,wBAAwB,EAAE,CAAC;AASjD,SAAS,UAAU,CAAC,KAAa;IAC/B,IAAI,0BAA0B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3C,OAAO,KAAK,CAAC;IACf,CAAC;IACD,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC;AAC7C,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAwB;IAC7D,MAAM,UAAU,GAAG,aAAa,CAAC,WAAW,CAAC;IAC7C,OAAO;QACL,UAAU;QACV,oBAAoB,EAAE,yBAAyB,UAAU,CAAC,UAAU,CAAC,EAAE;QACvE,cAAc,EAAE,GAAG,UAAU,YAAY;QACzC,gBAAgB,EAAE,qBAAqB;KACxC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,IAAuB;IAC5D,OAAO,CAAC,GAAG,CAAC,6CAA6C,CAAC,CAAC;IAC3D,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IACjD,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,CAAC,oBAAoB,EAAE,CAAC,CAAC;IAC9D,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IACnD,OAAO,CAAC,GAAG,CAAC,8FAA8F,CAAC,CAAC;IAC5G,OAAO,CAAC,GAAG,CACT,oHAAoH,CACrH,CAAC;AACJ,CAAC"}

package/dist/cli/doctor-lint.js

@@ -1,13 +1,13 @@
 import { readFile, readdir } from "node:fs/promises";
 import path from "node:path";
-import { parseNote } from "../conventions/frontmatter.js";
-import { detectLinkIssues } from "../conventions/lint.js";
-import { aggregateDoctor, formatDoctorReport, formatLintReport, } from "../conventions/report.js";
-import { mapWithConcurrency, walkVaultMarkdown } from "../conventions/vault-walk.js";
-import { validateFrontmatter } from "../conventions/validate.js";
-import { loadOntology } from "../core/ontology/loader.js";
-import { resolveConcept } from "../core/ontology/resolver.js";
-import { resolveBundledAssetPaths } from "../core/runtime/assets.js";
+import { parseNote } from "../kernel/conventions/frontmatter.js";
+import { detectLinkIssues } from "../kernel/conventions/lint.js";
+import { aggregateDoctor, formatDoctorReport, formatLintReport, } from "../kernel/conventions/report.js";
+import { mapWithConcurrency, walkVaultMarkdown } from "../kernel/conventions/vault-walk.js";
+import { validateFrontmatter } from "../kernel/conventions/validate.js";
+import { loadOntology } from "../kernel/ontology/loader.js";
+import { resolveConcept } from "../kernel/ontology/resolver.js";
+import { resolveBundledAssetPaths } from "../kernel/runtime/assets.js";
 const bundledAssets = resolveBundledAssetPaths();
 export async function runDoctor(opts) {
     const { vault } = opts;

package/dist/cli/doctor-lint.js.map

@@ -1 +1 @@
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package/dist/cli/global-writeback.js

@@ -1,5 +1,5 @@
 import { stat } from "node:fs/promises";
-import { readGlobalConfig, writeGlobalConfig } from "../link/global-config.js";
+import { readGlobalConfig, writeGlobalConfig } from "../kernel/link/global-config.js";
 /**
  * Register `vault` in the global config (`<homeDir>/.oms/config.yaml`).
  * When `overwrite` is false, does nothing if a global config already exists

package/dist/cli/global-writeback.js.map

@@ -1 +1 @@
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+{"version":3,"file":"global-writeback.js","sourceRoot":"","sources":["../../src/cli/global-writeback.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAC;AACxC,OAAO,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AAatF;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CAAC,OAAmC;IAC3E,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAC9C,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,IAAI,QAAQ,CAAC;QACb,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,OAAO,CAAC,CAAC;QAC7C,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,kDAAkD,EAAE,CAAC;QACtF,CAAC;QACD,IAAI,QAAQ,KAAK,IAAI,EAAE,CAAC;YACtB,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,gCAAgC,EAAE,CAAC;QACpE,CAAC;IACH,CAAC;IACD,MAAM,iBAAiB,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,OAAO,CAAC,CAAC;IACxD,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;AACzB,CAAC;AAOD;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,0BAA0B,CAAC,OAAmC;IAClF,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC;IACjC,MAAM,QAAQ,GAAG,GAAG,CAAC,WAAW,CAAC,CAAC;IAClC,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3D,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,mBAAmB,EAAE,CAAC;IACvD,CAAC;IAED,IAAI,QAAQ,CAAC;IACb,IAAI,CAAC;QACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,OAAO,CAAC,CAAC;IAC7C,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,kDAAkD,EAAE,CAAC;IACtF,CAAC;IACD,IAAI,QAAQ,KAAK,IAAI,EAAE,CAAC;QACtB,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,gCAAgC,EAAE,CAAC;IACpE,CAAC;IAED,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,CAAC;QACnC,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;YACzB,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,yCAAyC,EAAE,CAAC;QAC7E,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,mDAAmD,EAAE,CAAC;IACvF,CAAC;IAED,MAAM,iBAAiB,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,EAAE,OAAO,CAAC,CAAC;IAClE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;AACzB,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,uBAAuB,CAC3C,MAA4C;IAE5C,IAAI,CAAC;QACH,OAAO,MAAM,MAAM,EAAE,CAAC;IACxB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,OAAO,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QACvE,OAAO,CAAC,KAAK,CAAC,0DAA0D,OAAO,GAAG,CAAC,CAAC;QACpF,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC;IAC3C,CAAC;AACH,CAAC"}

package/dist/cli/host-commands.d.ts

@@ -6,7 +6,7 @@
  * install, the global vault record), so they live together and away from the
  * router, which owns dispatch alone.
  */
-import { type RuntimeSelection } from "../install/hosts.js";
+import { type RuntimeSelection } from "../kernel/install/hosts.js";
 /** Everything the host commands need from the parsed argv, plus the adapter root. */
 export interface HostCommandContext {
     readonly vault: string;

package/dist/cli/host-commands.js

@@ -7,10 +7,28 @@
  * router, which owns dispatch alone.
  */
 import path from "node:path";
-import { formatHostOperationResults, formatHostOperationResultsJson, runHostOperation, } from "../install/hosts.js";
-import { formatUpdateResult, runUpdate } from "../update/update.js";
+import { formatHostOperationResults, formatHostOperationResultsJson, runHostOperation, hostSurfaceForRuntime, } from "../kernel/install/hosts.js";
+import { formatUpdateResult, runUpdate } from "../kernel/update/update.js";
+import { installClaude, uninstallClaude } from "../vendors/claude/claude.js";
+import { installCodex, uninstallCodex } from "../vendors/codex/codex.js";
+import { installHermes, uninstallHermes } from "../vendors/hermes/hermes.js";
 import { backfillGlobalVaultFromEnv, nonFatalGlobalWriteback, registerGlobalVault, } from "./global-writeback.js";
 import { readCurrentPackageVersion } from "./update-notice.js";
+async function runVendorHostOperation(options, runtime) {
+    const host = hostSurfaceForRuntime(runtime);
+    if (options.action === "install") {
+        if (runtime === "claude")
+            return installClaude(options, host);
+        if (runtime === "codex")
+            return installCodex(options, host);
+        return installHermes(options, host);
+    }
+    if (runtime === "claude")
+        return uninstallClaude(options);
+    if (runtime === "codex")
+        return uninstallCodex(options);
+    return uninstallHermes(options);
+}
 /** Persist the vault the install just configured into the global record. */
 async function recordInstalledVault(context) {
     if (context.vaultExplicit) {
@@ -34,7 +52,7 @@ export async function runInstallOrUninstall(action, context) {
         executeExternal: context.executeExternal,
         yes: context.yes,
         adapterRoot: context.adapterRoot,
-    });
+    }, runVendorHostOperation);
     console.log(context.json
         ? formatHostOperationResultsJson(results, context.dryRun)
         : formatHostOperationResults(results, context.dryRun));
@@ -80,7 +98,7 @@ export async function runUpdateReconcile(context) {
         executeExternal: context.executeExternal,
         yes: true,
         adapterRoot: context.adapterRoot,
-    });
+    }, runVendorHostOperation);
     console.log(context.json
         ? formatHostOperationResultsJson(results, context.dryRun)
         : formatHostOperationResults(results, context.dryRun));

package/dist/cli/host-commands.js.map

@@ -1 +1 @@
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+{"version":3,"file":"host-commands.js","sourceRoot":"","sources":["../../src/cli/host-commands.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EACL,0BAA0B,EAC1B,8BAA8B,EAC9B,gBAAgB,EAChB,qBAAqB,GAItB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EAAE,kBAAkB,EAAE,SAAS,EAAE,MAAM,4BAA4B,CAAC;AAC3E,OAAO,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AACzE,OAAO,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EACL,0BAA0B,EAC1B,uBAAuB,EACvB,mBAAmB,GACpB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,yBAAyB,EAAE,MAAM,oBAAoB,CAAC;AAkB/D,KAAK,UAAU,sBAAsB,CACnC,OAA+C,EAC/C,OAAoB;IAEpB,MAAM,IAAI,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAC;IAC5C,IAAI,OAAO,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;QACjC,IAAI,OAAO,KAAK,QAAQ;YAAE,OAAO,aAAa,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;QAC9D,IAAI,OAAO,KAAK,OAAO;YAAE,OAAO,YAAY,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;QAC5D,OAAO,aAAa,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IACtC,CAAC;IACD,IAAI,OAAO,KAAK,QAAQ;QAAE,OAAO,eAAe,CAAC,OAAO,CAAC,CAAC;IAC1D,IAAI,OAAO,KAAK,OAAO;QAAE,OAAO,cAAc,CAAC,OAAO,CAAC,CAAC;IACxD,OAAO,eAAe,CAAC,OAAO,CAAC,CAAC;AAClC,CAAC;AAED,4EAA4E;AAC5E,KAAK,UAAU,oBAAoB,CAAC,OAA2B;IAC7D,IAAI,OAAO,CAAC,aAAa,EAAE,CAAC;QAC1B,MAAM,uBAAuB,CAAC,GAAG,EAAE,CACjC,mBAAmB,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CACjG,CAAC;QACF,OAAO;IACT,CAAC;IACD,MAAM,uBAAuB,CAAC,GAAG,EAAE,CAAC,0BAA0B,CAAC,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC;AAC5G,CAAC;AAED,sEAAsE;AACtE,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,MAA+B,EAC/B,OAA2B;IAE3B,IAAI,MAAM,KAAK,WAAW,IAAI,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,qBAAqB,CAAC,KAAK,GAAG,EAAE,CAAC;QAC5G,OAAO,CAAC,KAAK,CAAC,sDAAsD,CAAC,CAAC;QACtE,OAAO,CAAC,CAAC;IACX,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,gBAAgB,CACpC;QACE,MAAM;QACN,OAAO,EAAE,OAAO,CAAC,OAAO,IAAI,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC;QACnE,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,UAAU,EAAE,OAAO,CAAC,UAAU;QAC9B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,eAAe,EAAE,OAAO,CAAC,eAAe;QACxC,GAAG,EAAE,OAAO,CAAC,GAAG;QAChB,WAAW,EAAE,OAAO,CAAC,WAAW;KACjC,EACD,sBAAsB,CACvB,CAAC;IACF,OAAO,CAAC,GAAG,CACT,OAAO,CAAC,IAAI;QACV,CAAC,CAAC,8BAA8B,CAAC,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC;QACzD,CAAC,CAAC,0BAA0B,CAAC,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,CACxD,CAAC;IAEF,IAAI,MAAM,KAAK,SAAS,IAAI,CAAC,OAAO,CAAC,MAAM;QAAE,MAAM,oBAAoB,CAAC,OAAO,CAAC,CAAC;IACjF,OAAO,CAAC,CAAC;AACX,CAAC;AAED,mDAAmD;AACnD,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,OAA2B;IAChE,IAAI,OAAO,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpC,OAAO,CAAC,KAAK,CAAC,oCAAoC,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACrF,OAAO,CAAC,CAAC;IACX,CAAC;IAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC;QAC7B,cAAc,EAAE,MAAM,yBAAyB,EAAE;QACjD,aAAa,EAAE,OAAO,CAAC,GAAG,CAAC,2BAA2B,CAAC;QACvD,OAAO,EAAE,OAAO,CAAC,OAAO,IAAI,KAAK;QACjC,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,KAAK,EAAE,OAAO,CAAC,WAAW;QAC1B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,GAAG,EAAE,OAAO,CAAC,GAAG;QAChB,eAAe,EAAE,OAAO,CAAC,eAAe;QACxC,SAAS,EAAE,OAAO,CAAC,SAAS;QAC5B,gBAAgB,EAAE;YAChB,OAAO,EAAE,OAAO,CAAC,QAAQ;YACzB,UAAU,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACnE;KACF,CAAC,CAAC;IACH,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC;IACxC,OAAO,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAChC,CAAC;AAED,iFAAiF;AACjF,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,OAA2B;IAClE,IAAI,OAAO,CAAC,GAAG,CAAC,sBAAsB,CAAC,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;QACnE,OAAO,CAAC,KAAK,CAAC,qEAAqE,CAAC,CAAC;QACrF,OAAO,CAAC,CAAC;IACX,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,gBAAgB,CACpC;QACE,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,OAAO,CAAC,OAAO,IAAI,KAAK;QACjC,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,eAAe,EAAE,OAAO,CAAC,eAAe;QACxC,GAAG,EAAE,IAAI;QACT,WAAW,EAAE,OAAO,CAAC,WAAW;KACjC,EACD,sBAAsB,CACvB,CAAC;IACF,OAAO,CAAC,GAAG,CACT,OAAO,CAAC,IAAI;QACV,CAAC,CAAC,8BAA8B,CAAC,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC;QACzD,CAAC,CAAC,0BAA0B,CAAC,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,CACxD,CAAC;IACF,OAAO,CAAC,CAAC;AACX,CAAC"}

package/dist/cli/link-command.d.ts

@@ -1,4 +1,4 @@
-import { type CreateVaultLinkResult } from "../link/link.js";
+import { type CreateVaultLinkResult } from "../kernel/link/link.js";
 export declare function formatLinkResult(result: CreateVaultLinkResult, conventionNotePath?: string): string;
 export declare function runLink(options: {
     readonly cwd: string;

package/dist/cli/link-command.js

@@ -1,5 +1,5 @@
-import { createVaultLink, LINKED_GITIGNORE_PATTERN, } from "../link/link.js";
-import { writeConventionUsageSection } from "../link/convention-note.js";
+import { createVaultLink, LINKED_GITIGNORE_PATTERN, } from "../kernel/link/link.js";
+import { writeConventionUsageSection } from "../kernel/link/convention-note.js";
 export function formatLinkResult(result, conventionNotePath) {
     const lines = ["Oh My Second Brain vault bridge ready."];
     lines.push(`  Vault:     ${result.record.vault}`);

package/dist/cli/link-command.js.map

@@ -1 +1 @@
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+{"version":3,"file":"link-command.js","sourceRoot":"","sources":["../../src/cli/link-command.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,eAAe,EACf,wBAAwB,GAEzB,MAAM,wBAAwB,CAAC;AAChC,OAAO,EAAE,2BAA2B,EAAE,MAAM,mCAAmC,CAAC;AAEhF,MAAM,UAAU,gBAAgB,CAC9B,MAA6B,EAC7B,kBAA2B;IAE3B,MAAM,KAAK,GAAa,CAAC,wCAAwC,CAAC,CAAC;IACnE,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC;IAClD,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,QAAQ,EAAE,CAAC,CAAC;IACzE,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC;QAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACrF,IAAI,MAAM,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC;QAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAC3F,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;IAChD,KAAK,CAAC,IAAI,CACR,MAAM,CAAC,gBAAgB;QACrB,CAAC,CAAC,sBAAsB,wBAAwB,EAAE;QAClD,CAAC,CAAC,gBAAgB,wBAAwB,kBAAkB,CAC/D,CAAC;IACF,IAAI,kBAAkB,KAAK,SAAS,EAAE,CAAC;QACrC,KAAK,CAAC,IAAI,CAAC,uBAAuB,kBAAkB,EAAE,CAAC,CAAC;IAC1D,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,OAM7B;IACC,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC;QAC3B,OAAO,CAAC,KAAK,CAAC,uEAAuE,CAAC,CAAC;QACvF,OAAO,CAAC,CAAC;IACX,CAAC;IACD,IAAI,OAAO,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACjC,OAAO,CAAC,KAAK,CAAC,mDAAmD,CAAC,CAAC;QACnE,OAAO,CAAC,CAAC;IACX,CAAC;IAED,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,eAAe,CAAC;YACnC,GAAG,EAAE,OAAO,CAAC,GAAG;YAChB,KAAK,EAAE,OAAO,CAAC,KAAK;YACpB,OAAO,EAAE,CAAC,GAAG,OAAO,CAAC,OAAO,CAAC;SAC9B,CAAC,CAAC;QACH,IAAI,kBAAsC,CAAC;QAC3C,IAAI,OAAO,CAAC,cAAc,KAAK,KAAK,EAAE,CAAC;YACrC,kBAAkB,GAAG,CAAC,MAAM,2BAA2B,CAAC,OAAO,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC;QACxG,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,MAAM,EAAE,kBAAkB,CAAC,CAAC,CAAC;QAC1D,OAAO,CAAC,CAAC;IACX,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,SAAS,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACjF,OAAO,CAAC,CAAC;IACX,CAAC;AACH,CAAC"}

package/dist/cli/linkify.js

@@ -9,50 +9,9 @@
  * `writeNote`, which keeps path safety, the concept contract, and the
  * postcondition read-back unduplicated here.
  */
-import { readFile } from "node:fs/promises";
-import path from "node:path";
-import { parseNote } from "../conventions/frontmatter.js";
-import { mapWithConcurrency, walkVaultMarkdown } from "../conventions/vault-walk.js";
-import { writeNote } from "../capture/safe.js";
-import { resolveConcept } from "../core/ontology/resolver.js";
-import { applyLinks, hashBody } from "../engine/linkify/apply.js";
-import { suggestLinks, termBoundNotes } from "../engine/linkify/suggest.js";
-import { validateVaultLintFolder } from "../engine/conventions/vault-lint.js";
-import { resolveActiveOntology } from "../ontology/active.js";
-/** Parallel note reads; the walk itself is cheap, contents are the hot cost. */
-const READ_CONCURRENCY = 16;
-/** Flatten an unknown frontmatter `aliases` value to trimmed non-empty strings. */
-function aliasStrings(value) {
-    if (Array.isArray(value))
-        return value.flatMap(aliasStrings);
-    if (typeof value !== "string")
-        return [];
-    const trimmed = value.trim();
-    return trimmed ? [trimmed] : [];
-}
-/** Read every markdown note in the vault, parsed into body + surface forms. */
-async function scanVault(vault, ontology) {
-    const paths = [];
-    for await (const notePath of walkVaultMarkdown(vault))
-        paths.push(notePath);
-    return mapWithConcurrency(paths, READ_CONCURRENCY, async (notePath) => {
-        const raw = await readFile(path.join(vault, notePath), "utf-8");
-        const parsed = parseNote(raw);
-        return {
-            path: notePath,
-            body: parsed.body,
-            concept: resolveConcept(ontology, notePath)?.concept ?? null,
-            aliases: aliasStrings(parsed.frontmatter["aliases"]),
-        };
-    });
-}
-/** True when `notePath` sits inside `folder` (or when no scope was requested). */
-function inScope(notePath, folder) {
-    return folder === undefined || notePath.startsWith(`${folder}/`);
-}
-function toTermNote(note) {
-    return { path: note.path, concept: note.concept, aliases: note.aliases };
-}
+import { linkifyVault } from "../kernel/link/workflow.js";
+import { validateVaultLintFolder } from "../kernel/engine/conventions/vault-lint.js";
+import { resolveActiveOntology } from "../kernel/ontology/active.js";
 function describeCandidate(candidate) {
     const ambiguity = candidate.ambiguous ? ` (ambiguous: ${candidate.rivalPaths.join(", ")})` : "";
     return `    ${candidate.matchedText} → ${candidate.renderedReplacement}  [${candidate.targetPath}]${ambiguity}`;
@@ -63,20 +22,6 @@ function reportNote(notePath, candidates) {
     for (const candidate of candidates)
         console.log(describeCandidate(candidate));
 }
-/** Persist one note's candidates through the capture kernel. */
-async function applyNote(vault, ontology, note, candidates) {
-    const result = await applyLinks({
-        body: note.body,
-        baseContentHash: hashBody(note.body),
-        accepted: candidates,
-        writeNote,
-        target: { target: { vault, source: "explicit" }, ontology, notePath: note.path },
-    });
-    if (result.applied)
-        return true;
-    console.error(`[oms] linkify skipped ${note.path}: ${result.reason}`);
-    return false;
-}
 /**
  * Scan (and optionally link) a vault, restricting link TARGETS to notes bound
  * to the `term` concept.
@@ -89,25 +34,25 @@ export async function runLinkify(options) {
     try {
         const { ontology } = await resolveActiveOntology(options.vault);
         await validateVaultLintFolder(options.vault, ontology, options.folder);
-        const notes = await scanVault(options.vault, ontology);
-        const targets = termBoundNotes(notes.map(toTermNote));
-        const scoped = notes.filter((note) => inScope(note.path, options.folder));
-        console.log(`\nOh My Second Brain linkify: ${String(scoped.length)} note(s) in scope, ${String(targets.length)} term note(s) available as link targets.`);
+        const workflow = await linkifyVault({ vault: options.vault, source: "explicit", ontology }, { folder: options.folder, apply: options.apply });
+        console.log(`\nOh My Second Brain linkify: ${String(workflow.notesInScope)} note(s) in scope, ${String(workflow.targetNotes)} term note(s) available as link targets.`);
         let candidateCount = 0;
         let appliedNotes = 0;
-        for (const note of scoped) {
-            const candidates = suggestLinks(note.body, targets, { notePath: note.path });
-            if (candidates.length === 0)
-                continue;
-            candidateCount += candidates.length;
-            reportNote(note.path, candidates);
-            if (options.apply && (await applyNote(options.vault, ontology, note, candidates))) {
-                appliedNotes++;
+        for (const proposal of workflow.candidates) {
+            candidateCount += proposal.candidates.length;
+            reportNote(proposal.notePath, proposal.candidates);
+            if (proposal.outcome !== undefined) {
+                if (proposal.outcome.result.applied) {
+                    appliedNotes++;
+                }
+                else {
+                    console.error(`[oms] linkify skipped ${proposal.notePath}: ${proposal.outcome.result.reason}`);
+                }
             }
         }
         console.log(options.apply
             ? `\n${String(candidateCount)} candidate(s); applied to ${String(appliedNotes)} note(s).\n`
-            : `\n${String(candidateCount)} candidate(s) proposed across ${String(scoped.length)} note(s). Report only — nothing was written. Re-run with --apply --yes to write.\n`);
+            : `\n${String(candidateCount)} candidate(s) proposed across ${String(workflow.notesInScope)} note(s). Report only — nothing was written. Re-run with --apply --yes to write.\n`);
         return 0;
     }
     catch (error) {

package/dist/cli/linkify.js.map

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