oh-my-second-brain 0.12.0 → 0.12.1

package/.claude-plugin/marketplace.json

@@ -10,7 +10,7 @@
     {
       "name": "oms",
       "description": "Oh My Second Brain convention layer for Obsidian vaults — capture, retrieve, and validate knowledge under a declared semantic convention.",
-      "version": "0.12.0",
+      "version": "0.12.1",
       "author": {
         "name": "gobeumsu",
         "email": "gobeumsu@gmail.com"
@@ -37,5 +37,5 @@
       ]
     }
   ],
-  "version": "0.12.0"
+  "version": "0.12.1"
 }

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "oms",
-  "version": "0.12.0",
+  "version": "0.12.1",
   "description": "Oh My Second Brain convention layer for Obsidian vaults — capture, retrieve, and validate knowledge under a declared semantic convention.",
   "author": {
     "name": "gobeumsu"

package/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "oms",
-  "version": "0.12.0",
+  "version": "0.12.1",
   "description": "Oh My Second Brain convention layer for Obsidian vaults — Codex native rules, skills, and MCP adapter.",
   "_note": "oms install writes Codex MCP config, installs ~/.codex/rules/oms.md, and installs ~/.codex/skills/oms-*.",
   "skills": "./assets/skills/",

package/CHANGELOG-assets.md

@@ -4,6 +4,8 @@ Skills, agents, templates, and host guidance changes belong here.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
 ## [0.12.0] - 2026-09-01
 
 - **Guidance now identifies `.oms/taxonomy.json` as the user-owned folder/link authority.**

package/CHANGELOG-cli.md

@@ -4,9 +4,11 @@ Changes to the `oms` command surface belong here.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
 ## [0.12.0] - 2026-09-01
 
-- **Breaking: `oms doctor` no longer accepts `.oms/taxonomy.yaml`.** It reports one conversion error for a YAML-only vault (or cleanup guidance when both files remain); run `oms setup` and approve the returned digest to publish `.oms/taxonomy.json`.
+- **Breaking: `oms doctor` no longer accepts `.oms/taxonomy.yaml`.** It reports one conversion error for a YAML-only vault (or fail-closed cleanup guidance when both files remain); run `oms setup` and approve the returned digest to publish `.oms/taxonomy.json`.
 
 ## [0.11.1] - 2026-09-01
 

package/CHANGELOG-kernel.md

@@ -4,9 +4,11 @@ Domain logic changes belong here.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
 ## [0.12.0] - 2026-09-01
 
-- **Breaking: template taxonomy authority moved from `.oms/taxonomy.yaml` to `.oms/taxonomy.json`.** Resolution, transaction manifests, signatures, and derived folder ontology read JSON only. Approved setup converts legacy YAML and removes it after publishing the JSON authority; rerun setup and approve its newly returned digest for existing vaults.
+- **Breaking: template taxonomy authority moved from `.oms/taxonomy.yaml` to `.oms/taxonomy.json`.** Resolution, transaction manifests, signatures, and derived folder ontology read JSON only. Approved setup converts legacy YAML and deletes it inside the durable, CAS-guarded transaction; rerun setup and approve its newly returned digest for existing vaults.
 
 ## [0.11.1] - 2026-09-01
 

package/CHANGELOG-mcp.md

@@ -4,6 +4,8 @@ MCP server tools and resources belong here.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
 ## [0.12.0] - 2026-09-01
 
 ## [0.11.1] - 2026-09-01

package/CHANGELOG-vendors.md

@@ -4,6 +4,8 @@ Per-host adapter and installer changes belong here.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
 ## [0.12.0] - 2026-09-01
 
 ## [0.11.1] - 2026-09-01

package/CHANGELOG.md

@@ -10,6 +10,12 @@ This aggregate changelog contains changes that span multiple layers.
 
 ## [Unreleased]
 
+## [0.12.1] - 2026-09-01
+
+### Fixed
+
+- **Legacy taxonomy conversion is fully transaction-bounded.** YAML cleanup joins the approval hash with CAS/rollback/resume/receipts, doctor never reads YAML, and simultaneous JSON+YAML authorities fail closed with cleanup guidance.
+
 ## [0.12.0] - 2026-09-01
 
 - **Breaking: taxonomy authority is JSON-only across setup and validation.** Vaults now publish `.oms/taxonomy.json`; setup converts a legacy YAML taxonomy only after approval, removes it on apply, and requires a newly approved digest because the signed authority path changes.

package/README.ko.md

@@ -8,7 +8,7 @@ Oh My Second Brain(`oms`)은 기존 Obsidian/Markdown 볼트를 노트 소유권
 - 각 템플릿은 경로·digest와 독립적인 안정적 `templateId`를 가지며, 볼트 전체의 `BaseContract` 하나를 상속한다.
 - `.obsidian/types.json`은 읽기 전용 타입 권위다.
 - 사용자 소유 온톨로지는 계속 활성 상태다. `.oms/template-policy.json`은 노트·필드 의미와 필수값, 형식, 허용값, 기본값, 이름 규칙, 정체성, 바인딩을 기록한다.
-- `.oms/taxonomy.yaml`은 폴더·링크 의미와 배치를 소유하며, 작성된 폴더 의미는 `folder-ontology` 검색 축으로 노출된다.
+- `.oms/taxonomy.json`은 폴더·링크 의미와 배치를 소유하며, 작성된 폴더 의미는 `folder-ontology` 검색 축으로 노출된다. runtime의 유일한 권위이며, setup이 레거시 YAML을 한 번 변환한다.
 - `.oms/types.json`은 쓰기·검색용 검증된 파생 projection이다. 직접 편집하지 않는다.
 
 제거된 것은 노트 정체성으로서의 `concept`와 번들 runtime 기본값이지, 의미 계층으로서의 온톨로지가 아니다.

package/README.md

@@ -8,7 +8,7 @@ Oh My Second Brain (`oms`) connects an existing Obsidian or Markdown vault to AI
 - Each template has a stable `templateId`, independent of its path and digest, and inherits one vault-wide `BaseContract`.
 - `.obsidian/types.json` is read-only type authority.
 - The user-owned ontology remains active: `.oms/template-policy.json` records note/field meaning alongside requiredness, formats, allowed values, defaults, naming, identity, and bindings.
-- `.oms/taxonomy.yaml` records folder/link meaning and owns placement; authored folder intents are exposed through the `folder-ontology` search axis.
+- `.oms/taxonomy.json` records folder/link meaning and owns placement; authored folder intents are exposed through the `folder-ontology` search axis. It is the sole runtime authority; setup performs the one-time legacy YAML conversion.
 - `.oms/types.json` is a validated derived write/search projection. Never hand-edit it.
 
 The retired model is `concept` as note identity and bundled runtime defaults—not ontology as semantic meaning.

package/assets/hermes-manifest.json

@@ -1,6 +1,6 @@
 {
   "name": "oms",
-  "version": "0.12.0",
+  "version": "0.12.1",
   "description": "Oh My Second Brain convention layer for Obsidian vaults — Hermes skill bundle and MCP adapter.",
   "_note": "oms install writes ~/.hermes/config.yaml mcp_servers.oms and installs skills under ~/.hermes/skills/knowledge-management/oms/."
 }

package/dist/kernel/conventions/note-exclude.d.ts

@@ -6,6 +6,8 @@
 export declare const DEFAULT_EXCLUDE_GLOBS: readonly string[];
 /** True when `notePath` matches at least one of `globs`. */
 export declare function matchesAnyGlob(notePath: string, globs: readonly string[]): boolean;
+/** Setup migration injects a legacy declaration here; runtime readers stay JSON-only. */
+export declare function noteExcludeMatcherFromGlobs(globs: readonly string[]): (notePath: string) => boolean;
 /** Exact managed template paths without requiring the derived projection. */
 export declare function managedSourcePathSet(vaultRoot: string): Promise<ReadonlySet<string>>;
 /**

package/dist/kernel/conventions/note-exclude.js

@@ -51,6 +51,11 @@ function globToRegExp(glob) {
 export function matchesAnyGlob(notePath, globs) {
     return globs.some((glob) => globToRegExp(glob).test(notePath));
 }
+/** Setup migration injects a legacy declaration here; runtime readers stay JSON-only. */
+export function noteExcludeMatcherFromGlobs(globs) {
+    const matchers = [...DEFAULT_EXCLUDE_GLOBS, ...globs].map(globToRegExp);
+    return (notePath) => matchers.some((matcher) => matcher.test(normalizedPath(notePath)));
+}
 /** One resolve per vault root per process; every walker level shares it. */
 const matcherCache = new Map();
 function normalizedPath(notePath) {

package/dist/kernel/conventions/note-exclude.js.map

@@ -1 +1 @@
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package/dist/kernel/templates/canonical.d.ts

@@ -4,5 +4,8 @@ export declare function parseDigest(value: string): Digest;
 export declare function frameHash(domain: string, value: unknown): Uint8Array;
 export declare function hashCanonical(domain: string, value: unknown): Digest;
 export declare function inputDigest(input: InputV2): Digest;
-export declare function approvalDigest(input: Digest, operations: readonly LogicalOperation[], diagnostics: readonly Diagnostic[]): Digest;
+export declare function approvalDigest(input: Digest, operations: readonly LogicalOperation[], diagnostics: readonly Diagnostic[], cleanup?: {
+    readonly path: string;
+    readonly expectedDigest: Digest;
+}): Digest;
 export declare function outputDigest(outputs: readonly PlannedPhysicalOutput[]): Digest;

package/dist/kernel/templates/canonical.js

@@ -147,7 +147,7 @@ function diagnostic(value) {
         extensions: value.extensions ?? null,
     };
 }
-export function approvalDigest(input, operations, diagnostics) {
+export function approvalDigest(input, operations, diagnostics, cleanup) {
     parseDigest(input);
     const canonicalOperations = [...operations]
         .sort((left, right) => compare(left.kind, right.kind) ||
@@ -173,6 +173,7 @@ export function approvalDigest(input, operations, diagnostics) {
         inputDigest: input,
         operations: canonicalOperations,
         diagnostics: canonicalDiagnostics,
+        cleanup: cleanup === undefined ? null : { path: cleanup.path, expectedDigest: parseDigest(cleanup.expectedDigest) },
     });
 }
 export function outputDigest(outputs) {

package/dist/kernel/templates/canonical.js.map

@@ -1 +1 @@
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package/dist/kernel/templates/doctor.js

@@ -1,10 +1,10 @@
 import { createHash } from "node:crypto";
-import { readFile } from "node:fs/promises";
-import { join, resolve } from "node:path";
+import { lstat, readdir, readFile } from "node:fs/promises";
+import { join, relative, resolve } from "node:path";
 import { admitWriteTarget } from "../capture/safe.js";
 import { approvalDigest, inputDigest, outputDigest } from "./canonical.js";
 import { parseNote } from "../conventions/frontmatter.js";
-import { planTemplateMigration } from "./migration.js";
+import { excludedNoteMatcher } from "../conventions/note-exclude.js";
 import { normalizeTemplateSourcePath, verifyTemplateSourcePath } from "./paths.js";
 import { parseDerivedProjection, parseTemplatePolicy } from "./policy.js";
 import { buildTemplateCompositionManifest, loadResolvedTemplates } from "./resolver.js";
@@ -36,6 +36,38 @@ async function admitted(target) {
         : rejected("migration-incomplete", "resume or repair the validated template migration transaction before reading or repairing conventions");
 }
 function code(error) { return error instanceof Error ? error.message.split(":", 1)[0] ?? "TEMPLATE_DOCTOR_INVALID" : "TEMPLATE_DOCTOR_INVALID"; }
+async function exists(vault, path) {
+    try {
+        return (await lstat(join(vault, path))).isFile();
+    }
+    catch (error) {
+        if (error instanceof Error && "code" in error && error.code === "ENOENT")
+            return false;
+        throw error;
+    }
+}
+async function invalidNotes(vault) {
+    const excluded = await excludedNoteMatcher(vault, false);
+    const invalid = [];
+    const visit = async (directory) => {
+        for (const entry of await readdir(directory, { withFileTypes: true })) {
+            if (entry.name.startsWith("."))
+                continue;
+            const absolute = join(directory, entry.name);
+            if (entry.isDirectory()) {
+                await visit(absolute);
+                continue;
+            }
+            if (!entry.isFile() || !entry.name.endsWith(".md"))
+                continue;
+            const path = relative(vault, absolute).replaceAll("\\", "/");
+            if (!excluded(path) && parseNote(await readFile(absolute, "utf8")).diagnostics.length > 0)
+                invalid.push(path);
+        }
+    };
+    await visit(vault);
+    return invalid.sort();
+}
 /** Read-only health report for template authorities, projection, legacy notes, and transaction state. */
 export async function diagnoseTemplates(target) {
     const root = resolve(target.vault);
@@ -49,6 +81,21 @@ export async function diagnoseTemplates(target) {
             migrationMarker,
         };
     }
+    const [jsonExists, yamlExists] = await Promise.all([exists(root, ".oms/taxonomy.json"), exists(root, ".oms/taxonomy.yaml")]);
+    if (!jsonExists && yamlExists) {
+        return { status: "needs-repair", diagnostics: [{ code: "LEGACY_TAXONOMY_MIGRATION_REQUIRED", path: ".oms/taxonomy.yaml", remediation: "run setup to convert the legacy taxonomy exactly once" }], managedSourceExclusions: [], unresolvedLegacyNotes: [], migrationMarker };
+    }
+    if (jsonExists && yamlExists) {
+        return { status: "needs-repair", diagnostics: [{ code: "LEGACY_TAXONOMY_CONFLICT", path: ".oms/taxonomy.yaml", remediation: ".oms/taxonomy.json is authoritative; manually remove .oms/taxonomy.yaml" }], managedSourceExclusions: [], unresolvedLegacyNotes: [], migrationMarker };
+    }
+    if (jsonExists) {
+        try {
+            JSON.parse(await readFile(join(root, ".oms/taxonomy.json"), "utf8"));
+        }
+        catch {
+            return { status: "needs-repair", diagnostics: [{ code: "TEMPLATE_SOURCE_INVALID", path: ".oms/taxonomy.json", remediation: "restore valid .oms/taxonomy.json, then rerun doctor" }], managedSourceExclusions: [], unresolvedLegacyNotes: [], migrationMarker };
+        }
+    }
     const diagnostics = [];
     let policy = null;
     try {
@@ -71,10 +118,8 @@ export async function diagnoseTemplates(target) {
             diagnostics.push({ code: code(error), remediation: "run regenerate-types after correcting the named authority or template source" });
         }
     }
-    const proposal = await planTemplateMigration(root, { templateFolder: policy?.templateFolder });
-    const unresolvedLegacyNotes = proposal.existingNotes.filter(note => note.templateId === null && note.legacyConcept !== null).map(note => note.path);
-    for (const item of proposal.unresolved)
-        diagnostics.push({ code: item.code, ...(item.path === undefined ? {} : { path: item.path }), ...(item.templateId === undefined ? {} : { templateId: item.templateId }), remediation: "resolve this legacy mapping explicitly with backfill-defaults" });
+    for (const path of await invalidNotes(root))
+        diagnostics.push({ code: "MIGRATION_NOTE_INVALID", path, remediation: "repair the note frontmatter before migration" });
     const unique = new Map();
     for (const item of diagnostics)
         unique.set(`${item.code}\0${item.path ?? ""}`, item);
@@ -87,7 +132,7 @@ export async function diagnoseTemplates(target) {
         counts.set(key, count + 1);
         return count < target.maxPerTemplate;
     });
-    return { status: unique.size === 0 ? "healthy" : "needs-repair", diagnostics: bounded, managedSourceExclusions: proposal.managedSourcePaths, unresolvedLegacyNotes, migrationMarker };
+    return { status: unique.size === 0 ? "healthy" : "needs-repair", diagnostics: bounded, managedSourceExclusions: policy === null ? [] : Object.values(policy.templates).map(binding => binding.sourcePath), unresolvedLegacyNotes: [], migrationMarker };
 }
 /** Recomputes only the derived projection and delegates all publication to the guarded transaction. */
 export async function regenerateTypes(input) {

package/dist/kernel/templates/doctor.js.map

@@ -1 +1 @@
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package/dist/kernel/templates/migration.d.ts

@@ -50,6 +50,7 @@ export interface MigrationProposal {
 export interface MigrationOptions {
     readonly templateFolder?: string;
     readonly registeredTemplates?: readonly RegisteredTemplate[];
+    readonly legacyExclude?: readonly string[];
 }
 /** Read-only migration preflight. It preserves every legacy byte as a ledger entry and performs no publication. */
 export declare function planTemplateMigration(vault: string, options?: MigrationOptions): Promise<MigrationProposal>;

package/dist/kernel/templates/migration.js

@@ -1,9 +1,9 @@
 import { createHash } from "node:crypto";
-import { lstat, readdir, readFile, rm } from "node:fs/promises";
+import { lstat, readdir, readFile } from "node:fs/promises";
 import { basename, join, relative, resolve } from "node:path";
 import { parseDocument } from "yaml";
 import { parseNote } from "../conventions/frontmatter.js";
-import { excludedNoteMatcher } from "../conventions/note-exclude.js";
+import { excludedNoteMatcher, noteExcludeMatcherFromGlobs } from "../conventions/note-exclude.js";
 import { approvalDigest, inputDigest, outputDigest } from "./canonical.js";
 import { parseTemplate } from "./extract.js";
 import { parseTemplatePolicy, serializeDerivedProjection, serializeTemplatePolicy } from "./policy.js";
@@ -153,9 +153,19 @@ function conceptsFromTaxonomy(entries, diagnostics) {
     }
     return values.sort((left, right) => left.concept.localeCompare(right.concept) || left.folder.localeCompare(right.folder));
 }
-async function notes(root, sources, diagnostics) {
+function excludesFromTaxonomy(entries) {
+    const entry = entries.find(value => value.source === ".oms/taxonomy.yaml");
+    if (entry === undefined)
+        return [];
+    const document = parseDocument(new TextDecoder().decode(entry.bytes), { prettyErrors: false });
+    const root = mapping(document.toJS({ mapAsMap: true }));
+    const exclude = root?.get("exclude");
+    return Array.isArray(exclude) && exclude.every(value => typeof value === "string") ? exclude : [];
+}
+async function notes(root, sources, diagnostics, legacyExclude) {
     const values = [];
-    const isExcluded = await excludedNoteMatcher(root, false);
+    const runtimeExcluded = await excludedNoteMatcher(root, false);
+    const legacyExcluded = legacyExclude === undefined ? null : noteExcludeMatcherFromGlobs(legacyExclude);
     const visit = async (directory) => {
         for (const entry of await readdir(directory, { withFileTypes: true })) {
             if (entry.name.startsWith("."))
@@ -168,7 +178,7 @@ async function notes(root, sources, diagnostics) {
             if (!entry.isFile() || !entry.name.endsWith(".md"))
                 continue;
             const path = relative(root, absolute).replaceAll("\\", "/");
-            if (sources.has(path) || isExcluded(path))
+            if (sources.has(path) || runtimeExcluded(path) || legacyExcluded?.(path))
                 continue;
             const content = await readFile(absolute, "utf8");
             const parsed = parseNote(content);
@@ -215,6 +225,16 @@ export async function planTemplateMigration(vault, options = {}) {
         paths.add(candidate.sourcePath);
     }
     const legacyLedger = await ledger(root);
+    if (legacyLedger.some(entry => entry.path === ".oms/taxonomy.yaml")) {
+        try {
+            await readFile(join(root, ".oms", "taxonomy.json"));
+            diagnostics.push(issue("MIGRATION_TAXONOMY_INVALID", ".oms/taxonomy.json is authoritative; manually remove .oms/taxonomy.yaml before setup", ".oms/taxonomy.yaml"));
+        }
+        catch (error) {
+            if (!isMissing(error))
+                throw error;
+        }
+    }
     const taxonomyBindings = conceptsFromTaxonomy(legacyLedger, diagnostics);
     const byConcept = new Map();
     for (const candidate of candidates)
@@ -270,7 +290,7 @@ export async function planTemplateMigration(vault, options = {}) {
             ...candidates.map(candidate => candidate.sourcePath),
         ])].sort();
     const effectiveIds = new Set(candidates.map(candidate => candidate.templateId));
-    const existingNotes = await notes(root, new Set(managedSourcePaths), diagnostics);
+    const existingNotes = await notes(root, new Set(managedSourcePaths), diagnostics, options.legacyExclude ?? excludesFromTaxonomy(legacyLedger));
     const managedFolders = new Set(taxonomyBindings.map(binding => binding.folder.replace(/\/+$/g, "")));
     for (const note of existingNotes) {
         const stableNoteId = note.templateId === null ? null : stableId(note.templateId);
@@ -348,9 +368,6 @@ export async function applyTemplateMigration(vault, proposal, manifest, request)
         || typeof manifest.outputDigest !== "string")
         throw new Error("MIGRATION_APPROVAL_MISMATCH");
     const receipt = await executeTemplateTransaction(vault, manifest, request);
-    if (request.dryRun !== true && (receipt.status === "applied" || receipt.status === "already-complete")) {
-        await rm(join(vault, ".oms", "taxonomy.yaml"), { force: true });
-    }
     return receipt;
 }
 export function migrationProposalDigest(proposal) {
@@ -677,6 +694,8 @@ export async function buildMigrationManifest(vault, proposal, input) {
     if (authority === null)
         throw new Error("MIGRATION_AUTHORITY_MISSING: .obsidian/types.json");
     const currentPolicy = policyState.state === "present" ? parseTemplatePolicy(new TextDecoder().decode(policyState.bytes)) : undefined;
+    if (legacyTaxonomyState.state === "present" && taxonomyState.state === "present")
+        throw new Error("MIGRATION_TAXONOMY_CONFLICT: .oms/taxonomy.json is authoritative; manually remove .oms/taxonomy.yaml");
     const taxonomyInput = legacyTaxonomyState.state === "present" ? legacyTaxonomyState : taxonomyState;
     if (taxonomyInput.state === "present") {
         try {
@@ -756,7 +775,8 @@ export async function buildMigrationManifest(vault, proposal, input) {
     ];
     const mode = currentPolicy === undefined ? "create" : "update";
     const operations = proposedBindings.map(binding => ({ kind: mode, templateId: binding.templateId, destinationClass: binding.destinationClass, payloadDigest: candidateById.get(binding.templateId).bytes ? sha(candidateById.get(binding.templateId).bytes) : sha(new Uint8Array()), stableRelativeSuffix: null }));
-    const outputs = [...controls.map(control => ({ finalVaultRelativePath: control.path, payloadDigest: control.proposed.signature })), ...sources.map(source => ({ finalVaultRelativePath: source.path, payloadDigest: source.proposed.signature }))];
-    return { version: 1, mode, current, proposed, controls, sources, operations, diagnostics: [], moves: [], outputs, approvalDigest: approvalDigest(proposed.inputDigest, operations, []), outputDigest: outputDigest(outputs) };
+    const cleanup = legacyTaxonomyState.state === "present" ? { path: ".oms/taxonomy.yaml", expectedCurrent: expectation(legacyTaxonomyState), current: legacyTaxonomyState, proposed: { state: "absent" }, action: "delete" } : undefined;
+    const outputs = [...controls.map(control => ({ finalVaultRelativePath: control.path, payloadDigest: control.proposed.signature })), ...sources.map(source => ({ finalVaultRelativePath: source.path, payloadDigest: source.proposed.signature })), ...(cleanup?.expectedCurrent.state === "present" ? [{ finalVaultRelativePath: cleanup.path, payloadDigest: cleanup.expectedCurrent.signature }] : [])];
+    return { version: 1, mode, current, proposed, controls, sources, ...(cleanup === undefined ? {} : { legacyCleanup: cleanup }), operations, diagnostics: [], moves: [], outputs, approvalDigest: approvalDigest(proposed.inputDigest, operations, [], cleanup?.expectedCurrent.state === "present" ? { path: cleanup.path, expectedDigest: cleanup.expectedCurrent.signature } : undefined), outputDigest: outputDigest(outputs) };
 }
 //# sourceMappingURL=migration.js.map