oh-my-second-brain 0.2.0 → 0.3.0

package/dist/{harness → kernel/harness}/validation.js

@@ -14,13 +14,43 @@ const OWNERS = [
 const HOSTS = ["claude", "codex", "hermes"];
 const POSTURES = ["read", "write"];
 const STABILITIES = ["stable", "experimental", "compatibility"];
+/**
+ * Directory prefixes a shipped package path may live under.
+ *
+ * `assets/` holds all vendor runtime assets, including the single authored
+ * skill source and host-specific guidance, hooks, and rules.
+ */
 const PACKAGE_PATH_PREFIXES = [
-    "adapters/",
+    "assets/",
     "core/",
     "dist/",
     "docs/",
     "scripts/",
 ];
+/**
+ * Root-level files and directories that ship whole.
+ *
+ * The vendor plugin roots sit at the repository root because a host resolves a
+ * manifest's `skills` pointer relative to the manifest, and only a root-level
+ * manifest can reference `./assets/skills/` without climbing out of its own
+ * plugin root.
+ */
+const PACKAGE_ROOT_ENTRIES = [
+    ".claude-plugin",
+    ".codex-plugin",
+    ".mcp.json",
+    ".mcp.codex.json",
+    "package.json",
+];
+/**
+ * Root-level documents that legitimately ship.
+ *
+ * Changelogs are release history a consumer can read; ACKNOWLEDGMENTS carries
+ * the upstream credits the licence section points at, so shipping the licence
+ * note without it would leave a dangling reference in the published artifact.
+ * Contributor-only documents deliberately do NOT belong here.
+ */
+const PACKAGE_ROOT_DOCUMENT = /^(?:CHANGELOG(?:-[a-z]+)?|ACKNOWLEDGMENTS)\.md$/;
 function includesValue(values, value) {
     return typeof value === "string" && values.some((candidate) => candidate === value);
 }
@@ -67,6 +97,31 @@ function validateStability(violations, surface, stability) {
         });
     }
 }
+/**
+ * `adapterDir` names where a host's plugin manifest lives, which since the
+ * vendor topology move is decoupled from where its skills live. Claude and
+ * Codex read repo-root manifests, so `"."` is a legal and expected value here
+ * even though it is an unsafe segment in an ordinary package path.
+ *
+ * The legal set mirrors `resolveHostAdapterSource`'s allowlist exactly. Keeping
+ * it exhaustive rather than a prefix rule means there is no traversal to defend
+ * against: two literals cannot be escaped from.
+ */
+const LEGAL_ADAPTER_DIRS = [".", "assets"];
+function validateAdapterDir(violations, surface, adapterDir) {
+    if (typeof adapterDir !== "string" || adapterDir.length === 0) {
+        violations.push({ code: "missing_path", surface, message: `${surface} is missing a path.` });
+        return;
+    }
+    if (!LEGAL_ADAPTER_DIRS.some((legal) => legal === adapterDir)) {
+        violations.push({
+            code: "forbidden_path",
+            surface,
+            value: adapterDir,
+            message: `${surface} must be one of ${LEGAL_ADAPTER_DIRS.join(", ")}: ${adapterDir}`,
+        });
+    }
+}
 function validatePackagePath(violations, surface, path) {
     if (typeof path !== "string" || path.length === 0) {
         violations.push({ code: "missing_path", surface, message: `${surface} is missing a path.` });
@@ -86,6 +141,12 @@ function validatePackagePath(violations, surface, path) {
     const normalizedPath = pathPosix.normalize(path);
     if (normalizedPath === "package.json")
         return;
+    // `core/AGENTS.md` is the separately-owned vault-convention SSOT. It must SHIP
+    // - dropping it from the package silently removes an authoritative document -
+    // but nothing may treat it as a runtime asset or a release-verified artifact.
+    // So it is legal in npmFiles and rejected on every other surface.
+    if (normalizedPath === "core/AGENTS.md" && surface.startsWith("packageAssets.npmFiles"))
+        return;
     if (normalizedPath === "core/AGENTS.md" || normalizedPath.startsWith("src/")) {
         violations.push({
             code: "forbidden_path",
@@ -95,7 +156,10 @@ function validatePackagePath(violations, surface, path) {
         });
         return;
     }
-    if (!PACKAGE_PATH_PREFIXES.some((prefix) => normalizedPath === prefix.slice(0, -1) || normalizedPath.startsWith(prefix))) {
+    const underPrefix = PACKAGE_PATH_PREFIXES.some((prefix) => normalizedPath === prefix.slice(0, -1) || normalizedPath.startsWith(prefix));
+    const underRootEntry = PACKAGE_ROOT_ENTRIES.some((entry) => normalizedPath === entry || normalizedPath.startsWith(`${entry}/`));
+    const isRootDocument = PACKAGE_ROOT_DOCUMENT.test(normalizedPath);
+    if (!underPrefix && !underRootEntry && !isRootDocument) {
         violations.push({
             code: "forbidden_path",
             surface,
@@ -140,7 +204,6 @@ export function validateHarnessRegistry(registry) {
         validateOwner(violations, `cliCommands.${command.name}`, command.owner);
         validateStability(violations, `cliCommands.${command.name}`, command.stability);
     }
-    pushDuplicateViolations(violations, "coreSkillDirs", registry.coreSkillDirs, "duplicate_name");
     pushDuplicateViolations(violations, "mcpTools", registry.mcpTools.map((tool) => tool.name), "duplicate_name");
     for (const tool of registry.mcpTools) {
         validateOwner(violations, `mcpTools.${tool.name}`, tool.owner);
@@ -157,7 +220,7 @@ export function validateHarnessRegistry(registry) {
     pushDuplicateViolations(violations, "hosts", registry.hosts.map((host) => host.runtime), "duplicate_name");
     for (const host of registry.hosts) {
         validateRuntime(violations, `hosts.${host.runtime}`, host.runtime);
-        validatePackagePath(violations, `hosts.${host.runtime}.adapterDir`, host.adapterDir);
+        validateAdapterDir(violations, `hosts.${host.runtime}.adapterDir`, host.adapterDir);
         pushDuplicateViolations(violations, `hosts.${host.runtime}.skillDirs`, host.skillDirs.map((skillDir) => `${host.runtime}:${skillDir}`), "duplicate_name");
     }
     pushDuplicateViolations(violations, "hooks", registry.hooks.map((hook) => hook.bin), "duplicate_name");

package/dist/kernel/harness/validation.js.map

@@ -0,0 +1 @@
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package/dist/{index.d.ts → kernel/index.d.ts}

@@ -1,12 +1,11 @@
-export * from "./core/ontology/types.js";
-export * from "./core/ontology/loader.js";
-export * from "./core/ontology/resolver.js";
+export * from "./ontology/types.js";
+export * from "./ontology/loader.js";
+export * from "./ontology/resolver.js";
 export * from "./conventions/frontmatter.js";
 export * from "./conventions/validate.js";
 export * from "./graph/explore.js";
-export * from "./retrieve/semantic-contract.js";
+export * from "./search/semantic-contract.js";
 export * from "./engine/assemble.js";
-export * from "./retrieve/morning.js";
-export * from "./mcp/server.js";
+export * from "./search/morning.js";
 export * from "./harness/surface-registry.js";
 export * from "./harness/validation.js";

package/dist/kernel/index.js

@@ -0,0 +1,12 @@
+export * from "./ontology/types.js";
+export * from "./ontology/loader.js";
+export * from "./ontology/resolver.js";
+export * from "./conventions/frontmatter.js";
+export * from "./conventions/validate.js";
+export * from "./graph/explore.js";
+export * from "./search/semantic-contract.js";
+export * from "./engine/assemble.js";
+export * from "./search/morning.js";
+export * from "./harness/surface-registry.js";
+export * from "./harness/validation.js";
+//# sourceMappingURL=index.js.map

package/dist/kernel/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/kernel/index.ts"],"names":[],"mappings":"AAAA,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,2BAA2B,CAAC;AAC1C,cAAc,oBAAoB,CAAC;AACnC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,yBAAyB,CAAC"}

package/dist/{install → kernel/install}/adapter-source.d.ts

@@ -10,5 +10,14 @@ export declare class UnsupportedHostRuntimeError extends Error {
     readonly runtime: string;
     constructor(runtime: string);
 }
-export declare function resolveHostAdapterSource(adapterRoot: string, host: Pick<HarnessHostSurface, "runtime" | "adapterDir">): string;
+/**
+ * Resolve a host's manifest directory beneath `packageRoot`.
+ *
+ * Rejection order is load-bearing. `path.posix.normalize` collapses `assets/..`
+ * and `""` to `"."`, so a legal-value check placed before the traversal and
+ * emptiness checks would accept both. Every rejection therefore runs against
+ * the RAW value first, and only a value that survives all of them is compared
+ * against the allowlist.
+ */
+export declare function resolveHostAdapterSource(packageRoot: string, host: Pick<HarnessHostSurface, "runtime" | "adapterDir">): string;
 export declare function hostSurfaceForRuntime(runtime: HostRuntime): HarnessHostSurface;

package/dist/kernel/install/adapter-source.js

@@ -0,0 +1,76 @@
+import path from "node:path";
+import { harnessSurfaceRegistry } from "../harness/surface-registry.js";
+/**
+ * Exhaustive allowlist of legal `adapterDir` values.
+ *
+ * `adapterDir` names where a host's MANIFEST lives, which is now decoupled from
+ * where its skills live (the shared assets source). Claude and Codex read
+ * repo-root plugin manifests, so their manifest location is the repository root
+ * itself; Hermes has no repo plugin manifest and its metadata sits under
+ * `assets`.
+ *
+ * This is an exhaustive allowlist rather than a prefix rule on purpose. A
+ * prefix rule admits an open-ended family of paths and has to defend every one
+ * of them; two literal values cannot be traversed out of.
+ */
+const ALLOWED_ADAPTER_DIRS = [".", "assets"];
+export const HOST_RUNTIMES = harnessSurfaceRegistry.hosts.map((host) => host.runtime);
+export class HostAdapterSourceError extends Error {
+    runtime;
+    adapterDir;
+    constructor(host) {
+        super(`Invalid adapterDir for ${host.runtime}: ${host.adapterDir}`);
+        this.name = "HostAdapterSourceError";
+        this.runtime = host.runtime;
+        this.adapterDir = host.adapterDir;
+    }
+}
+export class UnsupportedHostRuntimeError extends Error {
+    runtime;
+    constructor(runtime) {
+        super(`Unsupported host runtime: ${runtime}`);
+        this.name = "UnsupportedHostRuntimeError";
+        this.runtime = runtime;
+    }
+}
+/**
+ * Resolve a host's manifest directory beneath `packageRoot`.
+ *
+ * Rejection order is load-bearing. `path.posix.normalize` collapses `assets/..`
+ * and `""` to `"."`, so a legal-value check placed before the traversal and
+ * emptiness checks would accept both. Every rejection therefore runs against
+ * the RAW value first, and only a value that survives all of them is compared
+ * against the allowlist.
+ */
+export function resolveHostAdapterSource(packageRoot, host) {
+    const raw = host.adapterDir;
+    // 1. Absolute paths escape the package entirely.
+    if (path.isAbsolute(raw) || path.win32.isAbsolute(raw)) {
+        throw new HostAdapterSourceError(host);
+    }
+    // 2. Empty is not a path. Checked on the raw value: normalize() turns "" into ".".
+    if (raw.trim().length === 0) {
+        throw new HostAdapterSourceError(host);
+    }
+    const slashed = raw.replace(/\\/g, "/");
+    // 3. Any traversal segment at all. Checked on the raw value: normalize() would
+    //    collapse "assets/.." to ".", which is itself a legal value, so deferring
+    //    this check until after normalization would silently admit it.
+    if (slashed.split("/").some((segment) => segment === "..")) {
+        throw new HostAdapterSourceError(host);
+    }
+    // 4. Only now is normalization safe: it can no longer mask a rejected input.
+    const normalized = path.posix.normalize(slashed).replace(/\/+$/, "") || ".";
+    if (!ALLOWED_ADAPTER_DIRS.includes(normalized)) {
+        throw new HostAdapterSourceError(host);
+    }
+    return normalized === "." ? packageRoot : path.join(packageRoot, normalized);
+}
+export function hostSurfaceForRuntime(runtime) {
+    const host = harnessSurfaceRegistry.hosts.find((candidate) => candidate.runtime === runtime);
+    if (host === undefined) {
+        throw new UnsupportedHostRuntimeError(runtime);
+    }
+    return host;
+}
+//# sourceMappingURL=adapter-source.js.map

package/dist/kernel/install/adapter-source.js.map

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

@@ -0,0 +1 @@
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package/dist/{install → kernel/install}/hosts.d.ts

@@ -1,9 +1,9 @@
 import type { HostOperationOptions, HostOperationResult, HostRuntime, RuntimeSelection } from "./types.js";
 export type { HostAction, HostOperationOptions, HostOperationResult, HostRuntime, RuntimeSelection, } from "./types.js";
-export { HostAdapterSourceError, UnsupportedHostRuntimeError, resolveHostAdapterSource } from "./adapter-source.js";
-export { buildGuardCommandString, isOmsHookEntry, removeClaudeHooks, replaceRootJsonPropertyPreservingBytes, toShellVaultPath, upsertClaudeHooks, } from "./claude-hooks.js";
+export { HostAdapterSourceError, UnsupportedHostRuntimeError, hostSurfaceForRuntime, resolveHostAdapterSource, } from "./adapter-source.js";
 export declare function detectAvailableHosts(): HostRuntime[];
 export declare function resolveRuntimeSelection(selection: RuntimeSelection): HostRuntime[];
-export declare function runHostOperation(options: HostOperationOptions): Promise<HostOperationResult[]>;
+export type HostOperationRunner = (options: HostOperationOptions, runtime: HostRuntime) => Promise<HostOperationResult>;
+export declare function runHostOperation(options: HostOperationOptions, runSingleHostOperation: HostOperationRunner): Promise<HostOperationResult[]>;
 export declare function formatHostOperationResults(results: readonly HostOperationResult[], dryRun?: boolean): string;
 export declare function formatHostOperationResultsJson(results: readonly HostOperationResult[], dryRun?: boolean): string;

package/dist/{install → kernel/install}/hosts.js

@@ -1,10 +1,6 @@
-import { hostSurfaceForRuntime, HOST_RUNTIMES } from "./adapter-source.js";
+import { HOST_RUNTIMES } from "./adapter-source.js";
 import { commandExists } from "./common.js";
-import { installClaude, uninstallClaude } from "./claude.js";
-import { installCodex, uninstallCodex } from "./codex.js";
-import { installHermes, uninstallHermes } from "./hermes.js";
-export { HostAdapterSourceError, UnsupportedHostRuntimeError, resolveHostAdapterSource } from "./adapter-source.js";
-export { buildGuardCommandString, isOmsHookEntry, removeClaudeHooks, replaceRootJsonPropertyPreservingBytes, toShellVaultPath, upsertClaudeHooks, } from "./claude-hooks.js";
+export { HostAdapterSourceError, UnsupportedHostRuntimeError, hostSurfaceForRuntime, resolveHostAdapterSource, } from "./adapter-source.js";
 export function detectAvailableHosts() {
     return HOST_RUNTIMES.filter((runtime) => commandExists(runtime));
 }
@@ -17,21 +13,6 @@ export function resolveRuntimeSelection(selection) {
     }
     return [selection];
 }
-async function runSingleHostOperation(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);
-}
 function failedHostOperationResult(options, runtime, error) {
     const reason = error instanceof Error ? error.message : String(error);
     return {
@@ -44,7 +25,7 @@ function failedHostOperationResult(options, runtime, error) {
         messages: [`FAILED: ${runtime} ${options.action} did not complete: ${reason}`],
     };
 }
-export async function runHostOperation(options) {
+export async function runHostOperation(options, runSingleHostOperation) {
     const runtimes = resolveRuntimeSelection(options.runtime);
     const results = [];
     for (const runtime of runtimes) {

package/dist/kernel/install/hosts.js.map

@@ -0,0 +1 @@
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package/dist/{core/ontology → kernel/install}/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/core/ontology/types.ts"],"names":[],"mappings":""}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/kernel/install/types.ts"],"names":[],"mappings":""}

package/dist/{link → kernel/link}/convention-note.js

@@ -18,9 +18,9 @@ export function conventionUsageSection(vaultPath) {
         "This repository is linked to an Oh My Second Brain vault. Use the linked vault as the project knowledge base when you need durable context.",
         "",
         `- Connected vault: ${renderedVaultName} (connection details live in .oms/links.yaml)`,
-        "- Query context: `oms query \"what context should I know for this change?\"`",
+        "- Query context: `oms semantic query \"what context should I know for this change?\"`",
         "- Search notes: `oms search \"keyword or topic\"`",
-        "- Open a note: `oms get \"note-id-or-path\"`",
+        "- Open a note: `oms semantic get \"note-id-or-path\"`",
         "- MCP integration: run `oms mcp` from this repository so compatible agents can read the linked vault through MCP.",
         CONVENTION_NOTE_END,
     ].join("\n");

package/dist/kernel/link/convention-note.js.map

@@ -0,0 +1 @@
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package/dist/kernel/link/global-config.js.map

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

@@ -0,0 +1 @@
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package/dist/kernel/link/workflow.d.ts

@@ -0,0 +1,55 @@
+import type { WriteTargetSource } from "../conventions/write-protocol.js";
+import { type ApplyResult } from "../engine/linkify/apply.js";
+import type { LinkCandidate, TermNote } from "../engine/linkify/types.js";
+import type { Ontology } from "../ontology/types.js";
+export interface ScannedLinkNote {
+    readonly path: string;
+    readonly body: string;
+    readonly concept: string | null;
+    readonly aliases: readonly string[];
+}
+export interface LinkWorkflowTarget {
+    readonly vault: string;
+    readonly source: WriteTargetSource;
+    readonly ontology: Ontology;
+    readonly notePath: string;
+}
+export interface LinkScope {
+    readonly folder?: string | undefined;
+}
+export interface IdentifiedLinkCandidate extends LinkCandidate {
+    readonly id: string;
+}
+export interface LinkSuggestion {
+    readonly notePath: string;
+    readonly baseContentHash: string;
+    readonly candidateNotes: number;
+    readonly candidates: readonly IdentifiedLinkCandidate[];
+}
+export interface LinkApplyOutcome {
+    readonly notePath: string;
+    readonly requestedIds: readonly string[];
+    readonly resolvedIds: readonly string[];
+    readonly result: ApplyResult;
+}
+export interface BatchLinkifyResult {
+    readonly notesInScope: number;
+    readonly targetNotes: number;
+    readonly candidates: readonly {
+        readonly notePath: string;
+        readonly candidates: readonly LinkCandidate[];
+        readonly outcome?: LinkApplyOutcome;
+    }[];
+}
+export declare function linkCandidateId(candidate: LinkCandidate): string;
+export declare function scanLinkNotes(vault: string, ontology: Ontology): Promise<ScannedLinkNote[]>;
+export declare function collectTermNotes(vault: string, ontology: Ontology, scope?: LinkScope): Promise<TermNote[]>;
+export declare function suggestLinksForNote(target: LinkWorkflowTarget, scope?: LinkScope): Promise<LinkSuggestion>;
+export declare function applyLinksForNote(target: LinkWorkflowTarget, selection: {
+    readonly baseContentHash: string;
+    readonly candidateIds: readonly string[];
+}, scope?: LinkScope): Promise<LinkApplyOutcome>;
+export declare function linkifyVault(target: Omit<LinkWorkflowTarget, "notePath">, options: {
+    readonly folder?: string;
+    readonly apply: boolean;
+}): Promise<BatchLinkifyResult>;

package/dist/kernel/link/workflow.js

@@ -0,0 +1,107 @@
+import { readFile } from "node:fs/promises";
+import path from "node:path";
+import { writeNote, safeVaultNotePath } from "../capture/safe.js";
+import { parseNote } from "../conventions/frontmatter.js";
+import { mapWithConcurrency, walkVaultMarkdown } from "../conventions/vault-walk.js";
+import { applyLinks, hashBody } from "../engine/linkify/apply.js";
+import { suggestLinks, termBoundNotes } from "../engine/linkify/suggest.js";
+import { resolveConcept } from "../ontology/resolver.js";
+const READ_CONCURRENCY = 16;
+function aliasStrings(value) {
+    if (Array.isArray(value))
+        return value.flatMap(aliasStrings);
+    if (typeof value !== "string")
+        return [];
+    const trimmed = value.trim();
+    return trimmed ? [trimmed] : [];
+}
+function inScope(notePath, folder) {
+    return folder === undefined || notePath.startsWith(`${folder}/`);
+}
+function toTermNote(note) {
+    return { path: note.path, concept: note.concept, aliases: note.aliases };
+}
+export function linkCandidateId(candidate) {
+    return `${String(candidate.startOffset)}-${String(candidate.endOffset)}`;
+}
+function identify(candidate) {
+    return { ...candidate, id: linkCandidateId(candidate) };
+}
+export async function scanLinkNotes(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"]),
+        };
+    });
+}
+async function readLinkNote(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 };
+}
+export async function collectTermNotes(vault, ontology, scope = {}) {
+    const notes = await scanLinkNotes(vault, ontology);
+    return termBoundNotes(notes.filter((note) => inScope(note.path, scope.folder)).map(toTermNote));
+}
+export async function suggestLinksForNote(target, scope = {}) {
+    const { normalized, body } = await readLinkNote(target.vault, target.notePath);
+    const notes = await collectTermNotes(target.vault, target.ontology, scope);
+    return {
+        notePath: normalized,
+        baseContentHash: hashBody(body),
+        candidateNotes: notes.length,
+        candidates: suggestLinks(body, notes, { notePath: normalized }).map(identify),
+    };
+}
+export async function applyLinksForNote(target, selection, scope = {}) {
+    const { normalized, body } = await readLinkNote(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(linkCandidateId(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(linkCandidateId), result };
+}
+export async function linkifyVault(target, options) {
+    const notes = await scanLinkNotes(target.vault, target.ontology);
+    const targets = termBoundNotes(notes.map(toTermNote));
+    const scoped = notes.filter((note) => inScope(note.path, options.folder));
+    const candidates = [];
+    for (const note of scoped) {
+        const proposed = suggestLinks(note.body, targets, { notePath: note.path });
+        if (proposed.length === 0)
+            continue;
+        let outcome;
+        if (options.apply) {
+            const result = await applyLinks({
+                body: note.body,
+                baseContentHash: hashBody(note.body),
+                accepted: proposed,
+                writeNote,
+                target: { target: { vault: target.vault, source: target.source }, ontology: target.ontology, notePath: note.path },
+            });
+            outcome = {
+                notePath: note.path,
+                requestedIds: proposed.map(linkCandidateId),
+                resolvedIds: proposed.map(linkCandidateId),
+                result,
+            };
+        }
+        candidates.push({ notePath: note.path, candidates: proposed, outcome });
+    }
+    return { notesInScope: scoped.length, targetNotes: targets.length, candidates };
+}
+//# sourceMappingURL=workflow.js.map

package/dist/kernel/link/workflow.js.map

@@ -0,0 +1 @@
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package/dist/{ontology → kernel/ontology}/active.d.ts

@@ -1,4 +1,4 @@
-import type { Ontology } from "../core/ontology/types.js";
+import type { Ontology } from "./types.js";
 export type ActiveOntologySource = "vault" | "bundled";
 export interface ActiveOntology {
     readonly ontology: Ontology;

package/dist/{ontology → kernel/ontology}/active.js

@@ -1,7 +1,7 @@
 import { stat } from "node:fs/promises";
 import path from "node:path";
-import { resolveBundledAssetPaths } from "../core/runtime/assets.js";
-import { loadOntology } from "../core/ontology/loader.js";
+import { resolveBundledAssetPaths } from "../runtime/assets.js";
+import { loadOntology } from "./loader.js";
 const bundledAssets = resolveBundledAssetPaths();
 async function pathKind(target) {
     try {

package/dist/kernel/ontology/active.js.map

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

@@ -0,0 +1 @@
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