oh-my-second-brain 0.1.9 → 0.2.0

package/dist/cli/global-writeback.js

@@ -0,0 +1,73 @@
+import { stat } from "node:fs/promises";
+import { readGlobalConfig, writeGlobalConfig } from "../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
+ * (including when reading the existing config throws, e.g. a corrupt file -
+ * a corrupt-but-present config is treated as "config exists, do not touch").
+ */
+export async function registerGlobalVault(options) {
+    const { vault, homeDir, overwrite } = options;
+    if (!overwrite) {
+        let existing;
+        try {
+            existing = await readGlobalConfig(homeDir);
+        }
+        catch {
+            return { wrote: false, reason: "existing global config is present but unreadable" };
+        }
+        if (existing !== null) {
+            return { wrote: false, reason: "existing global config present" };
+        }
+    }
+    await writeGlobalConfig({ version: 1, vault }, homeDir);
+    return { wrote: true };
+}
+/**
+ * Migration backfill: when no global config exists yet and `OMS_VAULT` points
+ * at an existing directory, register it. Never overwrites an existing config
+ * (including a corrupt-but-present one).
+ */
+export async function backfillGlobalVaultFromEnv(options) {
+    const { env, homeDir } = options;
+    const omsVault = env["OMS_VAULT"];
+    if (omsVault === undefined || omsVault.trim().length === 0) {
+        return { wrote: false, reason: "OMS_VAULT not set" };
+    }
+    let existing;
+    try {
+        existing = await readGlobalConfig(homeDir);
+    }
+    catch {
+        return { wrote: false, reason: "existing global config is present but unreadable" };
+    }
+    if (existing !== null) {
+        return { wrote: false, reason: "existing global config present" };
+    }
+    try {
+        const stats = await stat(omsVault);
+        if (!stats.isDirectory()) {
+            return { wrote: false, reason: "OMS_VAULT does not point at a directory" };
+        }
+    }
+    catch {
+        return { wrote: false, reason: "OMS_VAULT does not point at an existing directory" };
+    }
+    await writeGlobalConfig({ version: 1, vault: omsVault }, homeDir);
+    return { wrote: true };
+}
+/**
+ * Run a global write-back action, swallowing any failure into a single
+ * `[oms] warning:` line on stderr. Never throws.
+ */
+export async function nonFatalGlobalWriteback(action) {
+    try {
+        return await action();
+    }
+    catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        console.error(`[oms] warning: could not update global vault registry (${message})`);
+        return { wrote: false, reason: message };
+    }
+}
+//# sourceMappingURL=global-writeback.js.map

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

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

@@ -0,0 +1,30 @@
+/**
+ * Host-lifecycle CLI commands: `install`, `uninstall`, `update`, and the
+ * internal `update-reconcile`.
+ *
+ * These four are the only commands that mutate host adapter state (and, for
+ * 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";
+/** Everything the host commands need from the parsed argv, plus the adapter root. */
+export interface HostCommandContext {
+    readonly vault: string;
+    readonly vaultExplicit: boolean;
+    readonly runtime: RuntimeSelection | undefined;
+    readonly agentVault: string | undefined;
+    readonly dryRun: boolean;
+    readonly executeExternal: boolean;
+    readonly yes: boolean;
+    readonly json: boolean;
+    readonly checkUpdate: boolean;
+    readonly timeoutMs: number | undefined;
+    readonly unknownFlags: readonly string[];
+    readonly adapterRoot: string;
+}
+/** `oms install` / `oms uninstall`. Returns the process exit code. */
+export declare function runInstallOrUninstall(action: "install" | "uninstall", context: HostCommandContext): Promise<number>;
+/** `oms update`. Returns the process exit code. */
+export declare function runUpdateCommand(context: HostCommandContext): Promise<number>;
+/** `oms update-reconcile` — internal; re-runs install after a package update. */
+export declare function runUpdateReconcile(context: HostCommandContext): Promise<number>;

package/dist/cli/host-commands.js

@@ -0,0 +1,89 @@
+/**
+ * Host-lifecycle CLI commands: `install`, `uninstall`, `update`, and the
+ * internal `update-reconcile`.
+ *
+ * These four are the only commands that mutate host adapter state (and, for
+ * install, the global vault record), so they live together and away from the
+ * 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 { backfillGlobalVaultFromEnv, nonFatalGlobalWriteback, registerGlobalVault, } from "./global-writeback.js";
+import { readCurrentPackageVersion } from "./update-notice.js";
+/** Persist the vault the install just configured into the global record. */
+async function recordInstalledVault(context) {
+    if (context.vaultExplicit) {
+        await nonFatalGlobalWriteback(() => registerGlobalVault({ vault: path.resolve(context.vault), homeDir: undefined, overwrite: true }));
+        return;
+    }
+    await nonFatalGlobalWriteback(() => backfillGlobalVaultFromEnv({ env: process.env, homeDir: undefined }));
+}
+/** `oms install` / `oms uninstall`. Returns the process exit code. */
+export async function runInstallOrUninstall(action, context) {
+    if (action === "uninstall" && !context.yes && !context.dryRun && process.env["OMS_NON_INTERACTIVE"] !== "1") {
+        console.error("[oms] Refusing uninstall without --yes or --dry-run.");
+        return 1;
+    }
+    const results = await runHostOperation({
+        action,
+        runtime: context.runtime ?? (action === "install" ? "auto" : "all"),
+        vault: context.vault,
+        agentVault: context.agentVault,
+        dryRun: context.dryRun,
+        executeExternal: context.executeExternal,
+        yes: context.yes,
+        adapterRoot: context.adapterRoot,
+    });
+    console.log(context.json
+        ? formatHostOperationResultsJson(results, context.dryRun)
+        : formatHostOperationResults(results, context.dryRun));
+    if (action === "install" && !context.dryRun)
+        await recordInstalledVault(context);
+    return 0;
+}
+/** `oms update`. Returns the process exit code. */
+export async function runUpdateCommand(context) {
+    if (context.unknownFlags.length > 0) {
+        console.error(`[oms] Unsupported update option: ${context.unknownFlags.join(", ")}`);
+        return 1;
+    }
+    const result = await runUpdate({
+        currentVersion: await readCurrentPackageVersion(),
+        latestVersion: process.env["OMS_UPDATE_LATEST_VERSION"],
+        runtime: context.runtime ?? "all",
+        vault: context.vault,
+        check: context.checkUpdate,
+        dryRun: context.dryRun,
+        yes: context.yes,
+        executeExternal: context.executeExternal,
+        timeoutMs: context.timeoutMs,
+        reconcileCommand: {
+            command: process.execPath,
+            argsPrefix: process.argv[1] === undefined ? [] : [process.argv[1]],
+        },
+    });
+    console.log(formatUpdateResult(result));
+    return result.success ? 0 : 1;
+}
+/** `oms update-reconcile` — internal; re-runs install after a package update. */
+export async function runUpdateReconcile(context) {
+    if (process.env["OMS_UPDATE_RECONCILE"] !== "1" && !context.dryRun) {
+        console.error("[oms] update-reconcile is internal; run `oms update --yes` instead.");
+        return 1;
+    }
+    const results = await runHostOperation({
+        action: "install",
+        runtime: context.runtime ?? "all",
+        vault: context.vault,
+        dryRun: context.dryRun,
+        executeExternal: context.executeExternal,
+        yes: true,
+        adapterRoot: context.adapterRoot,
+    });
+    console.log(context.json
+        ? formatHostOperationResultsJson(results, context.dryRun)
+        : formatHostOperationResults(results, context.dryRun));
+    return 0;
+}
+//# sourceMappingURL=host-commands.js.map

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

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package/dist/cli/linkify.d.ts

@@ -0,0 +1,23 @@
+/**
+ * `oms linkify` — batch retrofit of `[[wikilinks]]` over EXISTING vault notes.
+ *
+ * Report-only by default. Mutation requires BOTH `--apply` and `--yes`, checked
+ * before any note is read, so a half-typed command can never reach the disk.
+ *
+ * The command owns scope and reporting only: span detection stays in
+ * engine/linkify (pure), and every write goes through the capture kernel's
+ * `writeNote`, which keeps path safety, the concept contract, and the
+ * postcondition read-back unduplicated here.
+ */
+export interface LinkifyOptions {
+    readonly vault: string;
+    /** Restrict both scan and writes to one top-level vault folder. */
+    readonly folder?: string;
+    readonly apply: boolean;
+    readonly yes: boolean;
+}
+/**
+ * Scan (and optionally link) a vault, restricting link TARGETS to notes bound
+ * to the `term` concept.
+ */
+export declare function runLinkify(options: LinkifyOptions): Promise<number>;

package/dist/cli/linkify.js

@@ -0,0 +1,118 @@
+/**
+ * `oms linkify` — batch retrofit of `[[wikilinks]]` over EXISTING vault notes.
+ *
+ * Report-only by default. Mutation requires BOTH `--apply` and `--yes`, checked
+ * before any note is read, so a half-typed command can never reach the disk.
+ *
+ * The command owns scope and reporting only: span detection stays in
+ * engine/linkify (pure), and every write goes through the capture kernel's
+ * `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 };
+}
+function describeCandidate(candidate) {
+    const ambiguity = candidate.ambiguous ? ` (ambiguous: ${candidate.rivalPaths.join(", ")})` : "";
+    return `    ${candidate.matchedText} → ${candidate.renderedReplacement}  [${candidate.targetPath}]${ambiguity}`;
+}
+/** Print one note's proposals; returns how many candidates it had. */
+function reportNote(notePath, candidates) {
+    console.log(`\n  ${notePath}`);
+    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.
+ */
+export async function runLinkify(options) {
+    if (options.apply && !options.yes) {
+        console.error("[oms] linkify --apply rewrites notes in place; re-run with --yes to confirm. Nothing was written.");
+        return 1;
+    }
+    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, ${String(targets.length)} term note(s) available as link targets.`);
+        let candidateCount = 0;
+        let appliedNotes = 0;
+        for (const note of scoped) {
+            const candidates = suggestLinks(note.body, targets, { notePath: note.path });
+            if (candidates.length === 0)
+                continue;
+            candidateCount += candidates.length;
+            reportNote(note.path, candidates);
+            if (options.apply && (await applyNote(options.vault, ontology, note, candidates))) {
+                appliedNotes++;
+            }
+        }
+        console.log(options.apply
+            ? `\n${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`);
+        return 0;
+    }
+    catch (error) {
+        console.error(`[oms] linkify could not complete: ${error instanceof Error ? error.message : String(error)}`);
+        return 1;
+    }
+}
+//# sourceMappingURL=linkify.js.map

package/dist/cli/linkify.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"linkify.js","sourceRoot":"","sources":["../../src/cli/linkify.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACrF,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAE9D,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,4BAA4B,CAAC;AAClE,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAE5E,OAAO,EAAE,uBAAuB,EAAE,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAE,qBAAqB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,gFAAgF;AAChF,MAAM,gBAAgB,GAAG,EAAE,CAAC;AAkB5B,mFAAmF;AACnF,SAAS,YAAY,CAAC,KAAc;IAClC,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;IAC7D,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC;IAC7B,OAAO,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AAClC,CAAC;AAED,+EAA+E;AAC/E,KAAK,UAAU,SAAS,CAAC,KAAa,EAAE,QAAkB;IACxD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,IAAI,KAAK,EAAE,MAAM,QAAQ,IAAI,iBAAiB,CAAC,KAAK,CAAC;QAAE,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;IAE5E,OAAO,kBAAkB,CAAC,KAAK,EAAE,gBAAgB,EAAE,KAAK,EAAE,QAAQ,EAAE,EAAE;QACpE,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,QAAQ,CAAC,EAAE,OAAO,CAAC,CAAC;QAChE,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC;QAC9B,OAAO;YACL,IAAI,EAAE,QAAQ;YACd,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,OAAO,EAAE,cAAc,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,OAAO,IAAI,IAAI;YAC5D,OAAO,EAAE,YAAY,CAAC,MAAM,CAAC,WAAW,CAAC,SAAS,CAAC,CAAC;SACrD,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC;AAED,kFAAkF;AAClF,SAAS,OAAO,CAAC,QAAgB,EAAE,MAA0B;IAC3D,OAAO,MAAM,KAAK,SAAS,IAAI,QAAQ,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,CAAC,CAAC;AACnE,CAAC;AAED,SAAS,UAAU,CAAC,IAAiB;IACnC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC;AAC3E,CAAC;AAED,SAAS,iBAAiB,CAAC,SAAwB;IACjD,MAAM,SAAS,GAAG,SAAS,CAAC,SAAS,CAAC,CAAC,CAAC,gBAAgB,SAAS,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;IAChG,OAAO,OAAO,SAAS,CAAC,WAAW,MAAM,SAAS,CAAC,mBAAmB,MAAM,SAAS,CAAC,UAAU,IAAI,SAAS,EAAE,CAAC;AAClH,CAAC;AAED,sEAAsE;AACtE,SAAS,UAAU,CAAC,QAAgB,EAAE,UAAoC;IACxE,OAAO,CAAC,GAAG,CAAC,OAAO,QAAQ,EAAE,CAAC,CAAC;IAC/B,KAAK,MAAM,SAAS,IAAI,UAAU;QAAE,OAAO,CAAC,GAAG,CAAC,iBAAiB,CAAC,SAAS,CAAC,CAAC,CAAC;AAChF,CAAC;AAED,gEAAgE;AAChE,KAAK,UAAU,SAAS,CACtB,KAAa,EACb,QAAkB,EAClB,IAAiB,EACjB,UAAoC;IAEpC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC;QAC9B,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,eAAe,EAAE,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC;QACpC,QAAQ,EAAE,UAAU;QACpB,SAAS;QACT,MAAM,EAAE,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,IAAI,EAAE;KACjF,CAAC,CAAC;IACH,IAAI,MAAM,CAAC,OAAO;QAAE,OAAO,IAAI,CAAC;IAChC,OAAO,CAAC,KAAK,CAAC,yBAAyB,IAAI,CAAC,IAAI,KAAK,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IACtE,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,OAAuB;IACtD,IAAI,OAAO,CAAC,KAAK,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC;QAClC,OAAO,CAAC,KAAK,CAAC,mGAAmG,CAAC,CAAC;QACnH,OAAO,CAAC,CAAC;IACX,CAAC;IAED,IAAI,CAAC;QACH,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,qBAAqB,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;QAChE,MAAM,uBAAuB,CAAC,OAAO,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;QAEvE,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;QACvD,MAAM,OAAO,GAAG,cAAc,CAAC,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC;QAE1E,OAAO,CAAC,GAAG,CACT,iCAAiC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,sBAAsB,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,0CAA0C,CAC7I,CAAC;QAEF,IAAI,cAAc,GAAG,CAAC,CAAC;QACvB,IAAI,YAAY,GAAG,CAAC,CAAC;QACrB,KAAK,MAAM,IAAI,IAAI,MAAM,EAAE,CAAC;YAC1B,MAAM,UAAU,GAAG,YAAY,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,EAAE,EAAE,QAAQ,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;YAC7E,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC;gBAAE,SAAS;YACtC,cAAc,IAAI,UAAU,CAAC,MAAM,CAAC;YACpC,UAAU,CAAC,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC;YAClC,IAAI,OAAO,CAAC,KAAK,IAAI,CAAC,MAAM,SAAS,CAAC,OAAO,CAAC,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,EAAE,CAAC;gBAClF,YAAY,EAAE,CAAC;YACjB,CAAC;QACH,CAAC;QAED,OAAO,CAAC,GAAG,CACT,OAAO,CAAC,KAAK;YACX,CAAC,CAAC,KAAK,MAAM,CAAC,cAAc,CAAC,6BAA6B,MAAM,CAAC,YAAY,CAAC,aAAa;YAC3F,CAAC,CAAC,KAAK,MAAM,CAAC,cAAc,CAAC,iCAAiC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,oFAAoF,CAC1K,CAAC;QACF,OAAO,CAAC,CAAC;IACX,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,qCAAqC,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC7G,OAAO,CAAC,CAAC;IACX,CAAC;AACH,CAAC"}

package/dist/cli/oms.d.ts

@@ -4,5 +4,6 @@ export type { ClaudeInstallPlan } from "./claude-install-plan.js";
 export { runDoctor, runLint } from "./doctor-lint.js";
 export { runAudit } from "./audit.js";
 export { formatLinkResult, runLink, } from "./link-command.js";
+export { runLinkify } from "./linkify.js";
 export { runSetup, type SetupPrompt, } from "./setup-command.js";
 export { maybePrintUpdateNotice } from "./update-notice.js";

package/dist/cli/oms.js

@@ -4,32 +4,32 @@ import path from "node:path";
 import { fileURLToPath } from "node:url";
 import { runPostToolUse } from "../hook/post-tool-use.js";
 import { runPreToolUse } from "../hook/pre-tool-use.js";
-import { formatHostOperationResults, formatHostOperationResultsJson, runHostOperation, } from "../install/hosts.js";
 import { resolveEffectiveVault } from "../link/link.js";
 import { runMcpServer } from "../mcp/server.js";
 import { resolveBundledAssetPaths } from "../core/runtime/assets.js";
-import { formatUpdateResult, runUpdate, } from "../update/update.js";
 import { parseCliArgs } from "./args.js";
 import { runAudit } from "./audit.js";
 import { runDoctor, runLint } from "./doctor-lint.js";
+import { runInstallOrUninstall, runUpdateCommand, runUpdateReconcile, } from "./host-commands.js";
+import { nonFatalGlobalWriteback, registerGlobalVault } from "./global-writeback.js";
 import { runLink } from "./link-command.js";
+import { runLinkify } from "./linkify.js";
 import { isSemanticCliCommand, runSemanticCli } from "./semantic.js";
 import { runSetup } from "./setup-command.js";
-import { maybePrintUpdateNotice, readCurrentPackageVersion } from "./update-notice.js";
+import { maybePrintUpdateNotice } from "./update-notice.js";
 import { printUsage } from "./usage.js";
 export { buildClaudeInstallPlan } from "./claude-install-plan.js";
 export { runDoctor, runLint } from "./doctor-lint.js";
 export { runAudit } from "./audit.js";
 export { formatLinkResult, runLink, } from "./link-command.js";
+export { runLinkify } from "./linkify.js";
 export { runSetup, } from "./setup-command.js";
 export { maybePrintUpdateNotice } from "./update-notice.js";
 const bundledAssets = resolveBundledAssetPaths();
-function bundledAdapterRoot() {
-    return bundledAssets.adapterRoot;
-}
 function shouldResolveBridgeVault(command, vaultExplicit) {
     return (!vaultExplicit &&
         (command === "audit" ||
+            command === "linkify" ||
             command === "doctor" ||
             command === "lint" ||
             command === "mcp" ||
@@ -43,12 +43,22 @@ async function main() {
         process.exitCode = 1;
         return;
     }
-    let { command, vault, vaultExplicit, yes, installClaude, suggestFields, runtime, dryRun, executeExternal, checkUpdate, timeoutMs, agentVault, verbose, json, maxPerConcept, folders, conventionNote, unknownFlags, } = parsedArgs;
-    if (shouldResolveBridgeVault(command, vaultExplicit)) {
+    let { command, vault, vaultExplicit, yes, apply, installClaude, suggestFields, runtime, dryRun, executeExternal, checkUpdate, timeoutMs, agentVault, verbose, json, maxPerConcept, folders, conventionNote, unknownFlags, } = parsedArgs;
+    // `mcp` keeps the FULL resolution result: the write surface trusts every
+    // source except `cwd`, so the server needs the source, not just the path.
+    let mcpTarget;
+    if (command === "mcp") {
+        mcpTarget = vaultExplicit
+            ? { vault, scope: null, source: "explicit" }
+            : await resolveEffectiveVault(process.cwd(), process.env);
+        vault = mcpTarget.vault;
+    }
+    else if (shouldResolveBridgeVault(command, vaultExplicit)) {
         vault = (await resolveEffectiveVault(process.cwd(), process.env)).vault;
     }
     if (command === "setup") {
         await runSetup({ vault, yes, installClaude, suggestFields });
+        await nonFatalGlobalWriteback(() => registerGlobalVault({ vault: path.resolve(vault), homeDir: undefined, overwrite: true }));
         await maybePrintUpdateNotice();
     }
     else if (command === "link") {
@@ -62,67 +72,15 @@ async function main() {
         await maybePrintUpdateNotice();
     }
     else if (command === "install" || command === "uninstall") {
-        const selectedRuntime = runtime ?? (command === "install" ? "auto" : "all");
-        if (command === "uninstall" && !yes && !dryRun && process.env["OMS_NON_INTERACTIVE"] !== "1") {
-            console.error("[oms] Refusing uninstall without --yes or --dry-run.");
-            process.exitCode = 1;
-            return;
-        }
-        const results = await runHostOperation({
-            action: command,
-            runtime: selectedRuntime,
-            vault,
-            agentVault,
-            dryRun,
-            executeExternal,
-            yes,
-            adapterRoot: bundledAdapterRoot(),
-        });
-        console.log(json ? formatHostOperationResultsJson(results, dryRun) : formatHostOperationResults(results, dryRun));
-        await maybePrintUpdateNotice();
+        process.exitCode = await runInstallOrUninstall(command, hostContext());
+        if (process.exitCode === 0)
+            await maybePrintUpdateNotice();
     }
     else if (command === "update") {
-        if (unknownFlags.length > 0) {
-            console.error(`[oms] Unsupported update option: ${unknownFlags.join(", ")}`);
-            process.exitCode = 1;
-            return;
-        }
-        const currentVersion = await readCurrentPackageVersion();
-        const latestVersion = process.env["OMS_UPDATE_LATEST_VERSION"];
-        const result = await runUpdate({
-            currentVersion,
-            latestVersion,
-            runtime: runtime ?? "all",
-            vault,
-            check: checkUpdate,
-            dryRun,
-            yes,
-            executeExternal,
-            timeoutMs,
-            reconcileCommand: {
-                command: process.execPath,
-                argsPrefix: process.argv[1] === undefined ? [] : [process.argv[1]],
-            },
-        });
-        console.log(formatUpdateResult(result));
-        process.exitCode = result.success ? 0 : 1;
+        process.exitCode = await runUpdateCommand(hostContext());
     }
     else if (command === "update-reconcile") {
-        if (process.env["OMS_UPDATE_RECONCILE"] !== "1" && !dryRun) {
-            console.error("[oms] update-reconcile is internal; run `oms update --yes` instead.");
-            process.exitCode = 1;
-            return;
-        }
-        const results = await runHostOperation({
-            action: "install",
-            runtime: runtime ?? "all",
-            vault,
-            dryRun,
-            executeExternal,
-            yes: true,
-            adapterRoot: bundledAdapterRoot(),
-        });
-        console.log(json ? formatHostOperationResultsJson(results, dryRun) : formatHostOperationResults(results, dryRun));
+        process.exitCode = await runUpdateReconcile(hostContext());
     }
     else if (command === "doctor") {
         process.exitCode = await runDoctor({ vault, verbose, json, maxPerConcept });
@@ -137,6 +95,15 @@ async function main() {
         });
         await maybePrintUpdateNotice();
     }
+    else if (command === "linkify") {
+        process.exitCode = await runLinkify({
+            vault,
+            folder: folders[0],
+            apply,
+            yes,
+        });
+        await maybePrintUpdateNotice();
+    }
     else if (command === "lint") {
         process.exitCode = await runLint({ vault, verbose, json });
         await maybePrintUpdateNotice();
@@ -149,7 +116,10 @@ async function main() {
         await maybePrintUpdateNotice();
     }
     else if (command === "mcp") {
-        await runMcpServer({ vault });
+        await runMcpServer({
+            vault,
+            source: mcpTarget?.source ?? "explicit",
+        });
     }
     else if (command === "hook") {
         const subcommand = argv[1];
@@ -169,6 +139,22 @@ async function main() {
         printUsage();
         process.exitCode = 0;
     }
+    function hostContext() {
+        return {
+            vault,
+            vaultExplicit,
+            runtime,
+            agentVault,
+            dryRun,
+            executeExternal,
+            yes,
+            json,
+            checkUpdate,
+            timeoutMs,
+            unknownFlags,
+            adapterRoot: bundledAssets.adapterRoot,
+        };
+    }
 }
 const __filename = fileURLToPath(import.meta.url);
 function sameEntrypoint(left, right) {

package/dist/cli/oms.js.map

@@ -1 +1 @@
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package/dist/cli/usage.js

@@ -16,6 +16,14 @@ const MAIN_USAGE_COMMANDS = [
     },
     { name: "lint", line: "  lint     Check vault link health: broken [[wikilinks]] and orphan notes." },
     { name: "link", line: "  link     Bridge an external repo to scoped vault folders via gitignored symlinks." },
+    {
+        name: "linkify",
+        line: "  linkify  Propose [[wikilinks]] to term notes across existing notes; report-only by default.",
+        detailLines: [
+            "             --folder <name>   Restrict the scan and writes to one top-level vault folder.",
+            "             --apply --yes     Rewrite notes in place; --apply alone refuses and writes nothing.",
+        ],
+    },
     { name: "semantic", line: "  semantic Native markdown semantic index/search/get commands." },
     { name: "mcp", line: "  mcp      Start the read/status MCP stdio server." },
     {
@@ -60,6 +68,7 @@ Usage:
   oh-my-second-brain audit [--vault <path>] [--folder <name>] [--json] [--suggest-fields]
   oh-my-second-brain lint [--vault <path>] [--verbose] [--json]
   oh-my-second-brain link --vault <path> --folder <name> [--folder <name> ...] [--no-convention-note]
+  oh-my-second-brain linkify [--vault <path>] [--folder <name>] [--apply --yes]
   oh-my-second-brain semantic <status|sync|query|search|vsearch|get|multi-get|collection> [options]
   oh-my-second-brain mcp [--vault <path>]
   oh-my-second-brain hook pre-tool-use [--vault <path>]
@@ -81,7 +90,8 @@ Options:
   --verbose        doctor/lint: list every affected note instead of a summary.
   --json           doctor/lint/audit: emit machine-readable output as JSON.
   --max <n>        doctor --verbose: max notes listed per concept (default 50).
-  --folder <name>  audit: restrict scan; link: vault folder/subpath to expose (repeatable for link).
+  --folder <name>  audit/linkify: restrict scan; link: vault folder/subpath to expose (repeatable for link).
+  --apply          linkify: rewrite notes in place; must be combined with --yes.
   --no-convention-note
                   link: skip writing the managed OMS usage block to AGENTS.md.
 `;

package/dist/cli/usage.js.map

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