oh-my-second-brain 0.2.0 → 0.3.0

package/dist/{cli/setup-documents.d.ts → kernel/setup/documents.d.ts}

@@ -1,4 +1,4 @@
-import type { Concept, FieldType, FolderBinding, OntologyField, OntologyLens, Taxonomy } from "../core/ontology/types.js";
+import type { Concept, FieldType, FolderBinding, OntologyField, OntologyLens, Taxonomy } from "../ontology/types.js";
 export interface ConceptDocument {
     readonly filePath: string;
     readonly raw: Record<string, unknown>;

package/dist/{cli/setup-documents.js → kernel/setup/documents.js}

@@ -58,35 +58,21 @@ export async function readConceptDocuments(omsDir) {
 }
 export function buildPromptConcepts(shippedConcepts, localDocuments) {
     const concepts = new Map(shippedConcepts);
-    for (const [name, document] of localDocuments) {
+    for (const [name, document] of localDocuments)
         concepts.set(name, document.concept);
-    }
     return concepts;
 }
 export function defaultConceptForFolder(concepts, folder) {
-    for (const [name, concept] of concepts) {
+    for (const [name, concept] of concepts)
         if (concept.folder === folder)
             return name;
-    }
     return null;
 }
 export function conceptRefToPromptDefault(concept) {
-    if (Array.isArray(concept))
-        return concept[0] ?? null;
-    return concept;
+    return Array.isArray(concept) ? (concept[0] ?? null) : concept;
 }
 export function isFieldType(value) {
-    switch (value) {
-        case "string":
-        case "url":
-        case "date":
-        case "list":
-        case "number":
-        case "boolean":
-            return true;
-        default:
-            return false;
-    }
+    return ["string", "url", "date", "list", "number", "boolean"].includes(value);
 }
 export async function readExistingTaxonomy(omsDir) {
     try {
@@ -94,20 +80,15 @@ export async function readExistingTaxonomy(omsDir) {
         const parsed = yamlParse(raw);
         if (!isRecord(parsed))
             return null;
-        const rawFolders = parsed["folders"];
         const folders = {};
-        if (isRecord(rawFolders)) {
-            for (const [folder, binding] of Object.entries(rawFolders)) {
+        if (isRecord(parsed["folders"])) {
+            for (const [folder, binding] of Object.entries(parsed["folders"])) {
                 const parsedBinding = parseFolderBinding(binding);
-                if (parsedBinding !== null) {
+                if (parsedBinding !== null)
                     folders[folder] = parsedBinding;
-                }
             }
         }
-        return {
-            version: typeof parsed["version"] === "number" ? parsed["version"] : 0,
-            folders,
-        };
+        return { version: typeof parsed["version"] === "number" ? parsed["version"] : 0, folders };
     }
     catch (error) {
         if (error instanceof Error)
@@ -117,33 +98,18 @@ export async function readExistingTaxonomy(omsDir) {
 }
 export function mergeAdditionalFields(concept, fields) {
     const existing = new Set(concept.fields.map((field) => field.name));
-    const additions = fields.filter((field) => !existing.has(field.name));
-    return {
-        ...concept,
-        fields: [...concept.fields, ...additions],
-        lenses: concept.lenses ?? [],
-    };
+    return { ...concept, fields: [...concept.fields, ...fields.filter((field) => !existing.has(field.name))], lenses: concept.lenses ?? [] };
 }
 export function mergeAdditionalLenses(concept, lenses) {
     const existing = new Set((concept.lenses ?? []).map((lens) => lens.name));
-    const additions = lenses.filter((lens) => !existing.has(lens.name));
-    return {
-        ...concept,
-        fields: concept.fields,
-        lenses: [...(concept.lenses ?? []), ...additions],
-    };
+    return { ...concept, fields: concept.fields, lenses: [...(concept.lenses ?? []), ...lenses.filter((lens) => !existing.has(lens.name))] };
 }
 export async function writeConcept(omsDir, concept, existingDocument) {
     const conceptsOutDir = path.join(omsDir, "concepts");
     await mkdir(conceptsOutDir, { recursive: true });
-    const document = {
-        ...(existingDocument?.raw ?? {}),
-        concept: concept.concept,
-        intent: concept.intent,
-        folder: concept.folder,
-        fields: concept.fields,
-        lenses: concept.lenses ?? [],
-    };
-    await writeFile(existingDocument?.filePath ?? path.join(conceptsOutDir, `${concept.concept}.yaml`), yamlStringify(document), "utf-8");
+    await writeFile(existingDocument?.filePath ?? path.join(conceptsOutDir, `${concept.concept}.yaml`), yamlStringify({
+        ...(existingDocument?.raw ?? {}), concept: concept.concept, intent: concept.intent, folder: concept.folder,
+        fields: concept.fields, lenses: concept.lenses ?? [],
+    }), "utf-8");
 }
-//# sourceMappingURL=setup-documents.js.map
+//# sourceMappingURL=documents.js.map

package/dist/kernel/setup/documents.js.map

@@ -0,0 +1 @@
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package/dist/kernel/setup/service.d.ts

@@ -0,0 +1,44 @@
+import type { Concept, FolderBinding, OntologyField, OntologyLens, Taxonomy } from "../ontology/types.js";
+import { type ObservedField, type ObservedFolderSummary } from "./axis.js";
+import { type ConceptDocument } from "./documents.js";
+export interface SetupState {
+    readonly vault: string;
+    readonly ontologyDir: string;
+    readonly omsDir: string;
+    readonly folders: readonly string[];
+    readonly existingTaxonomy: Taxonomy | null;
+    readonly promptConcepts: ReadonlyMap<string, Concept>;
+    readonly observedByFolder: ReadonlyMap<string, ObservedFolderSummary>;
+    readonly localConceptDocuments: ReadonlyMap<string, ConceptDocument>;
+    readonly bundledConceptFiles: readonly string[];
+}
+export interface SetupInputs {
+    readonly folderBindings: Readonly<Record<string, FolderBinding>>;
+    readonly observedFieldsByConcept?: ReadonlyMap<string, readonly ObservedField[]>;
+    readonly additionalFieldsByConcept?: ReadonlyMap<string, readonly OntologyField[]>;
+    readonly additionalLensesByConcept?: ReadonlyMap<string, readonly OntologyLens[]>;
+}
+export interface SetupDecision {
+    readonly vault: string;
+    readonly omsDir: string;
+    readonly ontologyDir: string;
+    readonly taxonomy: Taxonomy;
+    readonly bundledConceptFiles: readonly string[];
+    readonly concepts: readonly {
+        concept: Concept;
+        existingDocument?: ConceptDocument;
+    }[];
+}
+export declare function inspectSetup({ vault, ontologyDir }: {
+    vault: string;
+    ontologyDir: string;
+}): Promise<SetupState>;
+export declare function defaultSetupBinding(state: SetupState, folder: string): FolderBinding;
+export declare function decideSetup(state: SetupState, inputs: SetupInputs): SetupDecision;
+export declare function decideNonInteractiveSetup(state: SetupState, suggestFields: boolean): SetupDecision;
+export declare function applySetup(decision: SetupDecision, { dryRun }?: {
+    dryRun?: boolean;
+}): Promise<{
+    copiedFiles: readonly string[];
+    copyError?: unknown;
+}>;

package/dist/kernel/setup/service.js

@@ -0,0 +1,97 @@
+import { copyFile, mkdir, readFile, readdir, writeFile } from "node:fs/promises";
+import path from "node:path";
+import { stringify as yamlStringify } from "yaml";
+import { loadOntology } from "../ontology/loader.js";
+import { collectObservedFields, mergeObservedFieldsIntoConcept } from "./axis.js";
+import { buildPromptConcepts, conceptRefToPromptDefault, defaultConceptForFolder, mergeAdditionalFields, mergeAdditionalLenses, readConceptDocuments, readExistingTaxonomy, writeConcept, } from "./documents.js";
+export async function inspectSetup({ vault, ontologyDir }) {
+    const [ontology, observedSummaries, topEntries, existingTaxonomy, localConceptDocuments, conceptEntries] = await Promise.all([
+        loadOntology(ontologyDir),
+        collectObservedFields({ vault }),
+        readdir(vault, { withFileTypes: true }),
+        readExistingTaxonomy(path.join(vault, ".oms")),
+        readConceptDocuments(path.join(vault, ".oms")),
+        readdir(path.join(ontologyDir, "concepts")),
+    ]);
+    return {
+        vault, ontologyDir, omsDir: path.join(vault, ".oms"),
+        folders: topEntries.filter((entry) => entry.isDirectory() && !entry.name.startsWith(".")).map((entry) => entry.name),
+        existingTaxonomy,
+        promptConcepts: buildPromptConcepts(ontology.concepts, localConceptDocuments),
+        observedByFolder: new Map(observedSummaries.map((summary) => [summary.folder, summary])),
+        localConceptDocuments,
+        bundledConceptFiles: conceptEntries.filter((file) => file.endsWith(".yaml") || file.endsWith(".yml")),
+    };
+}
+export function defaultSetupBinding(state, folder) {
+    const existing = state.existingTaxonomy?.folders[folder];
+    return {
+        intent: existing?.intent || `${folder.charAt(0).toUpperCase()}${folder.slice(1)}`,
+        concept: conceptRefToPromptDefault(existing?.concept ?? null) ?? defaultConceptForFolder(state.promptConcepts, folder),
+    };
+}
+export function decideSetup(state, inputs) {
+    const observed = inputs.observedFieldsByConcept ?? new Map();
+    const additionalFields = inputs.additionalFieldsByConcept ?? new Map();
+    const additionalLenses = inputs.additionalLensesByConcept ?? new Map();
+    const names = new Set([...observed.keys(), ...additionalFields.keys(), ...additionalLenses.keys()]);
+    const concepts = [...names].flatMap((name) => {
+        const concept = state.promptConcepts.get(name);
+        if (concept === undefined)
+            return [];
+        return [{
+                concept: mergeAdditionalLenses(mergeAdditionalFields(mergeObservedFieldsIntoConcept(concept, observed.get(name) ?? []), additionalFields.get(name) ?? []), additionalLenses.get(name) ?? []),
+                existingDocument: state.localConceptDocuments.get(name),
+            }];
+    });
+    return {
+        vault: state.vault, omsDir: state.omsDir, ontologyDir: state.ontologyDir,
+        taxonomy: { version: state.existingTaxonomy?.version ?? 0, folders: { ...inputs.folderBindings } },
+        bundledConceptFiles: state.bundledConceptFiles,
+        concepts,
+    };
+}
+export function decideNonInteractiveSetup(state, suggestFields) {
+    const folderBindings = { ...(state.existingTaxonomy?.folders ?? {}) };
+    const observedFieldsByConcept = new Map();
+    for (const folder of state.folders) {
+        const binding = defaultSetupBinding(state, folder);
+        folderBindings[folder] = binding;
+        if (suggestFields && typeof binding.concept === "string") {
+            const fields = state.observedByFolder.get(folder)?.fields;
+            if (fields !== undefined)
+                observedFieldsByConcept.set(binding.concept, [...(observedFieldsByConcept.get(binding.concept) ?? []), ...fields]);
+        }
+    }
+    return decideSetup(state, { folderBindings, observedFieldsByConcept });
+}
+export async function applySetup(decision, { dryRun = false } = {}) {
+    if (dryRun)
+        return { copiedFiles: [] };
+    const conceptsOutDir = path.join(decision.omsDir, "concepts");
+    await mkdir(conceptsOutDir, { recursive: true });
+    await writeFile(path.join(decision.omsDir, "taxonomy.yaml"), yamlStringify(decision.taxonomy), "utf-8");
+    const copiedFiles = [];
+    let copyError;
+    try {
+        for (const file of decision.bundledConceptFiles) {
+            const target = path.join(conceptsOutDir, file);
+            try {
+                await readFile(target, "utf-8");
+            }
+            catch (error) {
+                if (!(error instanceof Error))
+                    throw error;
+                await copyFile(path.join(decision.ontologyDir, "concepts", file), target);
+                copiedFiles.push(file);
+            }
+        }
+    }
+    catch (error) {
+        copyError = error;
+    }
+    for (const { concept, existingDocument } of decision.concepts)
+        await writeConcept(decision.omsDir, concept, existingDocument);
+    return { copiedFiles, copyError };
+}
+//# sourceMappingURL=service.js.map

package/dist/kernel/setup/service.js.map

@@ -0,0 +1 @@
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package/dist/kernel/update/update.js.map

@@ -0,0 +1 @@
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package/dist/mcp/engine-morning-backend.d.ts

@@ -9,11 +9,11 @@
  * (graph-only context) rather than throwing.
  *
  * After the src/search teardown the morning contract types are the engine
- * contract types (re-exported via src/retrieve/semantic-contract.ts), so this
- * wrapper only threads the sync gate and the default vault — no type bridging.
+ * contract types (re-exported via src/kernel/search/semantic-contract.ts), so this
+ * wrapper only threads the default vault — no type bridging.
  */
-import type { McpEngineAdapter } from "../engine/mcp/facade.js";
-import type { MorningSemanticBackend } from "../retrieve/morning.js";
+import type { McpEngineAdapter } from "../kernel/engine/mcp/facade.js";
+import type { MorningSemanticBackend } from "../kernel/search/morning.js";
 /**
  * Build a MorningSemanticBackend that routes the five semantic leaf operations
  * through the native engine adapter.

package/dist/mcp/engine-morning-backend.js

@@ -9,8 +9,8 @@
  * (graph-only context) rather than throwing.
  *
  * After the src/search teardown the morning contract types are the engine
- * contract types (re-exported via src/retrieve/semantic-contract.ts), so this
- * wrapper only threads the sync gate and the default vault — no type bridging.
+ * contract types (re-exported via src/kernel/search/semantic-contract.ts), so this
+ * wrapper only threads the default vault — no type bridging.
  */
 /**
  * Build a MorningSemanticBackend that routes the five semantic leaf operations
@@ -25,22 +25,8 @@
  */
 export function makeEngineMorningBackend(adapter, vault) {
     return {
-        sync(opts) {
-            // Same R2 gate as before: never auto-sync unless the caller explicitly
-            // asked (syncBeforeSearch). Engine sync is incremental (SHA-256 diff), so
-            // even a forced re-sync skips unchanged chunks.
-            if (opts.semantic?.syncBeforeSearch !== true)
-                return Promise.resolve(undefined);
-            return adapter.syncEmbeddings({
-                vault: opts.vault ?? vault,
-                collection: opts.semantic.collection,
-                index: opts.semantic.index,
-                embed: opts.semantic.syncEmbed,
-                force: opts.semantic.syncForce,
-                chunkStrategy: opts.semantic.chunkStrategy,
-                maxDocsPerBatch: opts.semantic.syncMaxDocsPerBatch,
-                maxBatchMb: opts.semantic.syncMaxBatchMb,
-            });
+        sync() {
+            return Promise.resolve(undefined);
         },
         status(opts) {
             // semanticStatus is synchronous on the adapter; lift it into the async

package/dist/mcp/engine-morning-backend.js.map

@@ -1 +1 @@
-{"version":3,"file":"engine-morning-backend.js","sourceRoot":"","sources":["../../src/mcp/engine-morning-backend.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAKH;;;;;;;;;;GAUG;AACH,MAAM,UAAU,wBAAwB,CAAC,OAAyB,EAAE,KAAa;IAC/E,OAAO;QACL,IAAI,CAAC,IAA4B;YAC/B,uEAAuE;YACvE,0EAA0E;YAC1E,gDAAgD;YAChD,IAAI,IAAI,CAAC,QAAQ,EAAE,gBAAgB,KAAK,IAAI;gBAAE,OAAO,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAChF,OAAO,OAAO,CAAC,cAAc,CAAC;gBAC5B,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,KAAK;gBAC1B,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,UAAU;gBACpC,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,KAAK;gBAC1B,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS;gBAC9B,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS;gBAC9B,aAAa,EAAE,IAAI,CAAC,QAAQ,CAAC,aAAa;gBAC1C,eAAe,EAAE,IAAI,CAAC,QAAQ,CAAC,mBAAmB;gBAClD,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,cAAc;aACzC,CAAC,CAAC;QACL,CAAC;QAED,MAAM,CAAC,IAAI;YACT,uEAAuE;YACvE,oBAAoB;YACpB,OAAO,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC;QACvD,CAAC;QAED,KAAK,CAAC,IAAI;YACR,OAAO,OAAO,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;QACrC,CAAC;QAED,WAAW,CAAC,IAAI;YACd,OAAO,OAAO,CAAC,WAAW,CAAC,EAAE,GAAG,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,KAAK,EAAE,CAAC,CAAC;QACtE,CAAC;QAED,QAAQ,CAAC,IAAI;YACX,OAAO,OAAO,CAAC,iBAAiB,CAAC,EAAE,GAAG,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,KAAK,EAAE,OAAO,EAAE,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QACxG,CAAC;KACF,CAAC;AACJ,CAAC"}
+{"version":3,"file":"engine-morning-backend.js","sourceRoot":"","sources":["../../src/mcp/engine-morning-backend.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAKH;;;;;;;;;;GAUG;AACH,MAAM,UAAU,wBAAwB,CAAC,OAAyB,EAAE,KAAa;IAC/E,OAAO;QACL,IAAI;YACF,OAAO,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QACpC,CAAC;QAED,MAAM,CAAC,IAAI;YACT,uEAAuE;YACvE,oBAAoB;YACpB,OAAO,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC;QACvD,CAAC;QAED,KAAK,CAAC,IAAI;YACR,OAAO,OAAO,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;QACrC,CAAC;QAED,WAAW,CAAC,IAAI;YACd,OAAO,OAAO,CAAC,WAAW,CAAC,EAAE,GAAG,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,KAAK,EAAE,CAAC,CAAC;QACtE,CAAC;QAED,QAAQ,CAAC,IAAI;YACX,OAAO,OAAO,CAAC,iBAAiB,CAAC,EAAE,GAAG,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,KAAK,EAAE,OAAO,EAAE,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QACxG,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/mcp/link-tools.d.ts

@@ -1,78 +1,31 @@
-/**
- * MCP wiring for the linkify core: vault I/O + candidate universe for the
- * `oms_link_suggest` / `oms_link_apply` tools.
- *
- * The linkify core (mask → suggest → apply) is pure and dependency-injected; it
- * knows nothing about vaults, ontologies, or the filesystem. This module owns
- * exactly that translation and nothing else, so server.ts stays a dispatcher.
- *
- * Candidate identity is DERIVED, never cached. A candidate id is its body span,
- * and apply re-runs the same deterministic suggest pass over the note as it
- * exists right now. Two consequences that matter: the server holds no
- * cross-call state (a restart changes nothing), and a note edited between
- * suggest and apply is caught by the base-hash check the kernel-facing
- * `applyLinks` performs before any write.
- */
-import type { WriteTargetSource } from "../conventions/write-protocol.js";
-import type { Ontology } from "../core/ontology/types.js";
-import { type ApplyResult } from "../engine/linkify/apply.js";
-import type { LinkCandidate, TermNote } from "../engine/linkify/types.js";
+import type { ApplyResult } from "../kernel/engine/linkify/apply.js";
+import type { LinkCandidate } from "../kernel/engine/linkify/types.js";
+import { type LinkScope, type LinkWorkflowTarget } from "../kernel/link/workflow.js";
 /** A candidate as the MCP surface reports it: the core shape plus a stable id. */
 export interface IdentifiedCandidate extends LinkCandidate {
-    /** Deterministic handle a client passes back to `oms_link_apply`. */
     readonly id: string;
 }
 /** Payload of a successful `oms_link_suggest` call. */
 export interface LinkSuggestion {
     readonly notePath: string;
-    /** sha256 of the body the candidates were computed against (apply's token). */
     readonly baseContentHash: string;
     readonly candidateNotes: number;
     readonly candidates: readonly IdentifiedCandidate[];
 }
-/** Everything both link tools need to address a vault note. */
-export interface LinkToolTarget {
-    readonly vault: string;
-    readonly source: WriteTargetSource;
-    readonly ontology: Ontology;
-    /** Vault-relative markdown path of the note being linkified. */
-    readonly notePath: string;
-}
+/** Everything the MCP link operations need to address a vault note. */
+export type LinkToolTarget = LinkWorkflowTarget;
 /** Restrict the candidate universe to one top-level vault folder. */
-export interface LinkScope {
-    readonly folder?: string | undefined;
-}
-/**
- * Every `term`-bound note in the vault, with its declared surface forms.
- *
- * Concept binding comes from the ontology's folder contract (the same resolver
- * the write kernel uses), NOT from a frontmatter field a note can claim for
- * itself — a note cannot opt into being a link target by asserting it is one.
- */
-export declare function collectTermNotes(vault: string, ontology: Ontology, scope?: LinkScope): Promise<TermNote[]>;
-/**
- * Propose `[[wikilink]]` insertions for one note against the vault's term notes.
- *
- * Read-only: nothing is written and no state is retained. The returned
- * `baseContentHash` is the caller's optimistic-concurrency token for apply.
- */
-export declare function suggestLinksForNote(target: LinkToolTarget, scope?: LinkScope): Promise<LinkSuggestion>;
+export type { LinkScope };
 /** Payload of an `oms_link_apply` call: the core result plus what was selected. */
 export interface LinkApplyOutcome {
     readonly notePath: string;
     readonly requestedIds: readonly string[];
-    /** Requested ids that still name a live span in the note's current body. */
     readonly resolvedIds: readonly string[];
     readonly result: ApplyResult;
 }
-/**
- * Apply the selected candidates to a note and persist through the write kernel.
- *
- * The candidates are recomputed from the note's CURRENT body: ids that no
- * longer name a span simply do not resolve, and a body that drifted since
- * suggest fails the `baseContentHash` check inside `applyLinks` before any
- * write is attempted.
- */
+/** Invoke the transport-neutral suggestion workflow and retain the MCP contract. */
+export declare function suggestLinksForNote(target: LinkToolTarget, scope?: LinkScope): Promise<LinkSuggestion>;
+/** Invoke the transport-neutral apply workflow and retain the MCP contract. */
 export declare function applyLinksForNote(target: LinkToolTarget, selection: {
     readonly baseContentHash: string;
     readonly candidateIds: readonly string[];

package/dist/mcp/link-tools.js

@@ -1,135 +1,11 @@
-/**
- * MCP wiring for the linkify core: vault I/O + candidate universe for the
- * `oms_link_suggest` / `oms_link_apply` tools.
- *
- * The linkify core (mask → suggest → apply) is pure and dependency-injected; it
- * knows nothing about vaults, ontologies, or the filesystem. This module owns
- * exactly that translation and nothing else, so server.ts stays a dispatcher.
- *
- * Candidate identity is DERIVED, never cached. A candidate id is its body span,
- * and apply re-runs the same deterministic suggest pass over the note as it
- * exists right now. Two consequences that matter: the server holds no
- * cross-call state (a restart changes nothing), and a note edited between
- * suggest and apply is caught by the base-hash check the kernel-facing
- * `applyLinks` performs before any write.
- */
-import { readdir, readFile } from "node:fs/promises";
-import path from "node:path";
-import { safeVaultNotePath, writeNote } from "../capture/safe.js";
-import { parseNote } from "../conventions/frontmatter.js";
-import { resolveConcept } from "../core/ontology/resolver.js";
-import { applyLinks, hashBody } from "../engine/linkify/apply.js";
-import { suggestLinks, TERM_CONCEPT, termBoundNotes } from "../engine/linkify/suggest.js";
-/** A candidate id is the body span it claims — stable across identical bodies. */
-function candidateId(candidate) {
-    return `${String(candidate.startOffset)}-${String(candidate.endOffset)}`;
-}
-function identify(candidate) {
-    return { ...candidate, id: candidateId(candidate) };
-}
-/** Walk vault markdown, skipping dotted, dependency, and internal directories. */
-async function* walkMarkdown(dir, base) {
-    const entries = await readdir(dir, { withFileTypes: true });
-    for (const entry of entries) {
-        if (entry.name.startsWith(".") || entry.name === "node_modules")
-            continue;
-        const full = path.join(dir, entry.name);
-        if (entry.isDirectory()) {
-            yield* walkMarkdown(full, base);
-        }
-        else if (entry.isFile() && entry.name.endsWith(".md")) {
-            yield path.relative(base, full).replace(/\\/g, "/");
-        }
-    }
-}
-/** Flatten a 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] : [];
-}
-/**
- * Every `term`-bound note in the vault, with its declared surface forms.
- *
- * Concept binding comes from the ontology's folder contract (the same resolver
- * the write kernel uses), NOT from a frontmatter field a note can claim for
- * itself — a note cannot opt into being a link target by asserting it is one.
- */
-export async function collectTermNotes(vault, ontology, scope = {}) {
-    const root = scope.folder === undefined ? vault : path.join(vault, scope.folder);
-    const notes = [];
-    for await (const notePath of walkMarkdown(root, vault)) {
-        const concept = resolveConcept(ontology, notePath);
-        if (concept?.concept !== TERM_CONCEPT)
-            continue;
-        const raw = await readFile(path.join(vault, notePath), "utf-8");
-        notes.push({
-            path: notePath,
-            concept: concept.concept,
-            aliases: aliasStrings(parseNote(raw).frontmatter["aliases"]),
-        });
-    }
-    return termBoundNotes(notes);
-}
-/** Read one vault note's body, refusing unsafe paths and missing files loudly. */
-async function readNoteBody(vault, notePath) {
-    const fullPath = safeVaultNotePath(vault, notePath);
-    const raw = await readFile(fullPath, "utf-8");
-    return {
-        normalized: path.relative(vault, fullPath).replace(/\\/g, "/"),
-        body: parseNote(raw).body,
-    };
-}
-/**
- * Propose `[[wikilink]]` insertions for one note against the vault's term notes.
- *
- * Read-only: nothing is written and no state is retained. The returned
- * `baseContentHash` is the caller's optimistic-concurrency token for apply.
- */
+import { applyLinksForNote as applyWorkflowLinksForNote, suggestLinksForNote as suggestWorkflowLinksForNote, } from "../kernel/link/workflow.js";
+/** Invoke the transport-neutral suggestion workflow and retain the MCP contract. */
 export async function suggestLinksForNote(target, scope = {}) {
-    const { normalized, body } = await readNoteBody(target.vault, target.notePath);
-    const notes = await collectTermNotes(target.vault, target.ontology, scope);
-    const candidates = suggestLinks(body, notes, { notePath: normalized });
-    return {
-        notePath: normalized,
-        baseContentHash: hashBody(body),
-        candidateNotes: notes.length,
-        candidates: candidates.map(identify),
-    };
+    return suggestWorkflowLinksForNote(target, scope);
 }
-/**
- * Apply the selected candidates to a note and persist through the write kernel.
- *
- * The candidates are recomputed from the note's CURRENT body: ids that no
- * longer name a span simply do not resolve, and a body that drifted since
- * suggest fails the `baseContentHash` check inside `applyLinks` before any
- * write is attempted.
- */
+/** Invoke the transport-neutral apply workflow and retain the MCP contract. */
 export async function applyLinksForNote(target, selection, scope = {}) {
-    const { normalized, body } = await readNoteBody(target.vault, target.notePath);
-    const notes = await collectTermNotes(target.vault, target.ontology, scope);
-    const wanted = new Set(selection.candidateIds);
-    const accepted = suggestLinks(body, notes, { notePath: normalized }).filter((candidate) => wanted.has(candidateId(candidate)));
-    const result = await applyLinks({
-        body,
-        baseContentHash: selection.baseContentHash,
-        accepted,
-        writeNote,
-        target: {
-            target: { vault: target.vault, source: target.source },
-            ontology: target.ontology,
-            notePath: normalized,
-        },
-    });
-    return {
-        notePath: normalized,
-        requestedIds: selection.candidateIds,
-        resolvedIds: accepted.map(candidateId),
-        result,
-    };
+    return applyWorkflowLinksForNote(target, selection, scope);
 }
 /** The MCP-facing JSON shape of an apply outcome: applied body + receipt, or a typed refusal. */
 export function linkApplyPayload(outcome) {

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package/dist/mcp/server.d.ts

@@ -1,10 +1,17 @@
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { type Tool } from "@modelcontextprotocol/sdk/types.js";
-import type { WriteTargetSource } from "../conventions/write-protocol.js";
-export declare const BASE_SERVER_INSTRUCTIONS = "Oh My Second Brain exposes ontology/status/cache/retrieval tools and the write tool. write is gated by a verified vault target (a vault inferred from the current directory is refused), vault confinement, and contract validation.";
+import type { WriteTargetSource } from "../kernel/conventions/write-protocol.js";
+import type { Reranker } from "../kernel/engine/retrieval/reranker.js";
+export declare const BASE_SERVER_INSTRUCTIONS = "Oh My Second Brain exposes write, search, link, status, and doctor tools. oms_write and doctor repair operations are gated by a verified vault target (a vault inferred from the current directory is refused); oms_write also enforces vault confinement and contract validation.";
 export declare const omsMcpTools: Tool[];
 export interface OMSMcpServerOptions {
     vault: string;
+    /**
+     * Real cross-encoder used only for requests that explicitly set
+     * `rerank: true`. Without one, those requests fail rather than silently
+     * returning the unranked result.
+     */
+    reranker?: Reranker;
     /**
      * How the vault was resolved. The write surface trusts every source except
      * `cwd` (the server may have booted in an arbitrary directory - issue #58).