mdkg 0.1.2 → 0.1.3

package/CHANGELOG.md

@@ -4,6 +4,31 @@ All notable changes to mdkg are documented here.
 
 This project follows a pragmatic changelog style inspired by Keep a Changelog. Versions use npm package versions.
 
+## 0.1.3 - Unreleased
+
+### Added
+
+- Added first-class SQLite access cache support using Node's built-in `node:sqlite`; no third-party SQLite package is introduced.
+- Added `.mdkg/index/mdkg.sqlite` as a rebuildable derived cache for nodes, edges, skills, capabilities, archives, bundle imports, source hashes, and schema metadata when `index.backend` is `sqlite`.
+- Added fresh init defaults for `index.backend: sqlite`, `index.sqlite_path`, `index.sqlite_commit_warning_bytes`, and `index.lock_timeout_ms`.
+- Added a shared mutation lock plus atomic writes for mdkg mutations and index writes.
+- Added SQLite transactional id reservation for numeric node/checkpoint ids in SQLite mode.
+- Added `npm run smoke:sqlite` and `npm run smoke:parallel` packed/temp-repo coverage.
+
+### Changed
+
+- Raised the required Node runtime to `>=24.15.0`.
+- Existing workspaces that are migrated from older configs remain on `index.backend: json` until they explicitly opt in to SQLite.
+- Init ignore policy now keeps JSON indexes, temp files, lock directories, WAL, SHM, and journal files ignored while allowing `.mdkg/index/mdkg.sqlite` to be committed by intentional repo policy.
+- `mdkg index` continues to write JSON compatibility indexes and also rebuilds SQLite when enabled.
+- `mdkg doctor` and `mdkg validate` now report SQLite cache health when SQLite mode is enabled.
+- README and seeded docs now state that mdkg is pre-v1 public alpha software and cache/DAL contracts may churn before v1.
+
+### Fixed
+
+- Removed the accidental self-dependency on `mdkg` from package metadata.
+- Hardened parallel `mdkg new`, checkpoint, task, work, archive, bundle import config, and index writes against naming conflicts and partial cache writes.
+
 ## 0.1.2 - 2026-05-19
 
 ### Added

package/README.md

@@ -9,11 +9,14 @@ It is built for:
 
 mdkg stays deliberately boring:
 - repo-native under `.mdkg/`
-- TypeScript + Node.js 18+
-- zero runtime dependencies
-- no required sqlite, daemon, hosted index, or vector DB
+- TypeScript + Node.js `>=24.15.0`
+- zero third-party runtime dependencies
+- first-class rebuildable SQLite cache through built-in `node:sqlite`
+- no daemon, hosted index, or vector DB
 
-Current package version in source: `0.1.2`
+Current package version in source: `0.1.3`
+
+mdkg is still pre-v1 public alpha software. The public package is usable, but graph, cache, bundle, and DAL contracts may continue to change quickly while the project converges on a stable v1 surface.
 
 ## The product shape
 
@@ -202,10 +205,11 @@ mdkg lives under a hidden root directory:
 - `.mdkg/skills/` Agent Skills packages
 - `.mdkg/archive/` sidecar metadata plus deterministic compressed source/artifact caches
 - `.mdkg/bundles/` optional committed full graph snapshot bundles
+- `.mdkg/index/mdkg.sqlite` optional committed, rebuildable SQLite access cache
 - `.mdkg/index/imports.json` generated read-only bundle import cache
 - `.agents/skills/` Codex/OpenAI-facing mirrored skills
 - `.claude/skills/` Claude-facing mirrored skills
-- `.mdkg/index/` generated cache files
+- `.mdkg/index/*.json` generated JSON compatibility cache files
 
 ## Primary commands
 
@@ -292,6 +296,14 @@ The capability cache is not the full graph and is not source of truth. Normal ta
 
 Capability records aggregate enabled registered workspaces and include deterministic source metadata such as `workspace`, `visibility`, `kind`, `id`, `qid`, `path`, headings, refs, source hash, and `indexed_at`. Workspace `visibility` also feeds mdkg's export safety checks for public/internal packs and public bundles. This is a CLI safety layer, not secret scanning, body redaction, or a replacement for private git hosting.
 
+## Index backends and parallel safety
+
+Fresh `mdkg init` workspaces default to `index.backend: sqlite`, which writes `.mdkg/index/mdkg.sqlite` as a rebuildable access cache using Node's built-in `node:sqlite`. Existing workspaces that are migrated from older configs default to `index.backend: json` until they opt in. Markdown files, archive sidecars, bundle manifests, and config remain source of truth in both modes.
+
+`mdkg index` still writes JSON compatibility caches (`global.json`, `skills.json`, `capabilities.json`, and import projections when configured). In SQLite mode it also rebuilds the SQLite cache with nodes, edges, skills, capabilities, archive metadata, bundle imports, source hashes, and schema metadata. Deleting the SQLite file is recoverable with `mdkg index`.
+
+Mutating commands use a workspace mutation lock plus atomic writes. SQLite mode additionally reserves numeric ids in a SQLite transaction before writing Markdown so parallel `mdkg new` and checkpoint calls avoid naming conflicts. Skipped ids after failed writes are acceptable because Markdown remains canonical.
+
 ## Agent workflow files
 
 mdkg recognizes a small set of canonical agent workflow documents:
@@ -323,10 +335,12 @@ By default, init/upgrade ignore generated raw archive source copies with `.mdkg/
 
 This release includes:
 - `init --agent`
-- default ignore updates with `--no-update-ignores` for `.mdkg/index/`, `.mdkg/pack/`, and raw archive source copies
+- default ignore updates with `--no-update-ignores` for generated JSON index/temp/lock files, `.mdkg/pack/`, and raw archive source copies
 - root-only published init seed config
 - skills indexing and search/show/list support
 - JSON capability cache for skills, `SPEC.md`, `WORK.md`, core docs, and design docs
+- SQLite index backend for fresh workspaces using built-in `node:sqlite`
+- mutation locking and atomic writes for parallel mdkg calls
 - optional `skills: [...]` on work items
 - pack-time skill inclusion
 - latest-checkpoint resolver + index hint
@@ -360,7 +374,8 @@ Design and decision records live in the internal graph under `.mdkg/design/`.
 mdkg is not a secret store.
 
 Use these defaults:
-- keep `.mdkg/index/` gitignored
+- keep generated `.mdkg/index/*.json`, temp, lock, WAL, SHM, and journal files gitignored
+- commit `.mdkg/index/mdkg.sqlite` only when the repo intentionally tracks a reasonably sized rebuildable access cache
 - keep `.mdkg/pack/` gitignored
 - keep `.mdkg/archive/**/source/` gitignored unless a repo intentionally commits raw local copies
 - commit archive sidecar `.md` metadata and deterministic `.zip` caches when they are needed for reviewable evidence

package/dist/cli.js

@@ -171,6 +171,8 @@ function printIndexHelp(log) {
     log("  - .mdkg/index/global.json");
     log("  - .mdkg/index/skills.json");
     log("  - .mdkg/index/capabilities.json");
+    log("  - .mdkg/index/imports.json when bundle imports are configured");
+    log("  - .mdkg/index/mdkg.sqlite when index.backend is sqlite");
     printGlobalOptions(log);
 }
 function printShowHelp(log) {
@@ -544,6 +546,7 @@ function printDoctorHelp(log) {
     log("  - Bundle import health and staleness");
     log("  - Index load/rebuild health");
     log("  - Capability cache load/rebuild health");
+    log("  - SQLite cache health when enabled");
     log("\nOptions:");
     log("  --json                Emit machine-readable JSON output");
     printGlobalOptions(log);

package/dist/commands/archive.js

@@ -3,10 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.runArchiveAddCommand = runArchiveAddCommand;
 exports.runArchiveListCommand = runArchiveListCommand;
 exports.runArchiveShowCommand = runArchiveShowCommand;
 exports.runArchiveVerifyCommand = runArchiveVerifyCommand;
+exports.runArchiveAddCommand = runArchiveAddCommand;
 exports.runArchiveCompressCommand = runArchiveCompressCommand;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
@@ -15,11 +15,14 @@ const frontmatter_1 = require("../graph/frontmatter");
 const archive_integrity_1 = require("../graph/archive_integrity");
 const indexer_1 = require("../graph/indexer");
 const index_cache_1 = require("../graph/index_cache");
+const reindex_1 = require("../graph/reindex");
 const visibility_1 = require("../graph/visibility");
 const date_1 = require("../util/date");
 const errors_1 = require("../util/errors");
 const id_1 = require("../util/id");
 const refs_1 = require("../util/refs");
+const atomic_1 = require("../util/atomic");
+const lock_1 = require("../util/lock");
 const zip_1 = require("../util/zip");
 const event_support_1 = require("./event_support");
 const ARCHIVE_KINDS = new Set(["source", "artifact"]);
@@ -124,8 +127,7 @@ function maybeReindex(root) {
     if (!config.index.auto_reindex) {
         return;
     }
-    const outputPath = path_1.default.resolve(root, config.index.global_index_path);
-    (0, index_cache_1.writeIndex)(outputPath, (0, indexer_1.buildIndex)(root, config, { tolerant: config.index.tolerant }));
+    (0, reindex_1.writeDerivedIndexes)(root, config, (0, indexer_1.buildIndex)(root, config, { tolerant: config.index.tolerant }));
 }
 function resolveArchiveNode(root, id, ws) {
     const config = (0, config_1.loadConfig)(root);
@@ -174,7 +176,7 @@ function stringAttribute(value) {
 function writeArchiveSidecar(sidecarPath, frontmatter, body) {
     const lines = (0, frontmatter_1.formatFrontmatter)(frontmatter);
     const content = ["---", ...lines, "---", body.trimStart()].join("\n");
-    fs_1.default.writeFileSync(sidecarPath, content.endsWith("\n") ? content : `${content}\n`, "utf8");
+    (0, atomic_1.atomicWriteFile)(sidecarPath, content.endsWith("\n") ? content : `${content}\n`);
 }
 function verifyArchiveSidecar(root, ws, sidecarPath) {
     const relativePath = toPosixPath(path_1.default.relative(root, sidecarPath));
@@ -276,7 +278,7 @@ function loadArchiveVerifyResults(options) {
     }
     return results;
 }
-function runArchiveAddCommand(options) {
+function runArchiveAddCommandLocked(options) {
     const config = (0, config_1.loadConfig)(options.root);
     const ws = normalizeWorkspace(options.ws);
     const workspace = config.workspaces[ws];
@@ -311,7 +313,7 @@ function runArchiveAddCommand(options) {
     fs_1.default.copyFileSync(sourcePath, rawPath);
     const rawData = fs_1.default.readFileSync(rawPath);
     const zipData = (0, zip_1.createDeterministicZip)(basename, rawData);
-    fs_1.default.writeFileSync(zipPath, zipData);
+    (0, atomic_1.atomicWriteFile)(zipPath, zipData);
     const frontmatter = {
         id,
         type: "archive",
@@ -423,7 +425,7 @@ function runArchiveVerifyCommand(options) {
         throw new errors_1.ValidationError("archive verification failed");
     }
 }
-function runArchiveCompressCommand(options) {
+function runArchiveCompressCommandLocked(options) {
     if (!options.all && !options.id) {
         throw new errors_1.UsageError("archive compress requires <id-or-archive-uri> or --all");
     }
@@ -441,7 +443,7 @@ function runArchiveCompressCommand(options) {
         }
         const rawData = fs_1.default.readFileSync(rawPath);
         const zipData = (0, zip_1.createDeterministicZip)(path_1.default.basename(rawPath), rawData);
-        fs_1.default.writeFileSync(zipPath, zipData);
+        (0, atomic_1.atomicWriteFile)(zipPath, zipData);
         const parsed = (0, frontmatter_1.parseFrontmatter)(fs_1.default.readFileSync(sidecarPath, "utf8"), sidecarPath);
         const nextFrontmatter = {
             ...parsed.frontmatter,
@@ -472,3 +474,13 @@ function runArchiveCompressCommand(options) {
     }
     console.log(`archive compressed: ${updated.length}`);
 }
+function withArchiveLock(root, fn) {
+    const config = (0, config_1.loadConfig)(root);
+    return (0, lock_1.withMutationLock)(root, config.index.lock_timeout_ms, fn);
+}
+function runArchiveAddCommand(options) {
+    return withArchiveLock(options.root, () => runArchiveAddCommandLocked(options));
+}
+function runArchiveCompressCommand(options) {
+    return withArchiveLock(options.root, () => runArchiveCompressCommandLocked(options));
+}

package/dist/commands/bundle_import.js

@@ -16,6 +16,8 @@ const migrate_1 = require("../core/migrate");
 const workspace_path_1 = require("../core/workspace_path");
 const bundle_imports_1 = require("../graph/bundle_imports");
 const errors_1 = require("../util/errors");
+const atomic_1 = require("../util/atomic");
+const lock_1 = require("../util/lock");
 const ALIAS_RE = /^[a-z][a-z0-9_]*$/;
 function writeJson(value) {
     console.log(JSON.stringify(value, null, 2));
@@ -71,7 +73,7 @@ function readRawConfig(root) {
     return { configPath, raw: migrated };
 }
 function writeRawConfig(configPath, raw) {
-    fs_1.default.writeFileSync(configPath, `${JSON.stringify(raw, null, 2)}\n`, "utf8");
+    (0, atomic_1.atomicWriteFile)(configPath, `${JSON.stringify(raw, null, 2)}\n`);
 }
 function getImports(raw) {
     const imports = raw.bundle_imports;
@@ -98,7 +100,11 @@ function healthByAlias(root, alias) {
     }
     return health;
 }
-function runBundleImportAddCommand(options) {
+function withBundleImportLock(root, fn) {
+    const config = (0, config_1.loadConfig)(root);
+    return (0, lock_1.withMutationLock)(root, config.index.lock_timeout_ms, fn);
+}
+function runBundleImportAddCommandLocked(options) {
     const alias = normalizeAlias(options.alias);
     const bundlePath = normalizeContained(options.bundlePath, "bundle import path");
     const visibility = normalizeVisibility(options.visibility);
@@ -150,6 +156,9 @@ function runBundleImportAddCommand(options) {
         console.log(`warnings: ${health.warning_count}`);
     }
 }
+function runBundleImportAddCommand(options) {
+    return withBundleImportLock(options.root, () => runBundleImportAddCommandLocked(options));
+}
 function runBundleImportListCommand(options) {
     const config = (0, config_1.loadConfig)(options.root);
     const imports = (0, bundle_imports_1.buildBundleImportsIndex)(options.root, config).index.imports;
@@ -166,7 +175,7 @@ function runBundleImportListCommand(options) {
         console.log(`${item.alias} | ${status} | ${item.visibility} | ${item.path}`);
     }
 }
-function runBundleImportRemoveCommand(options) {
+function runBundleImportRemoveCommandLocked(options) {
     const alias = normalizeAlias(options.alias);
     const { configPath, raw } = readRawConfig(options.root);
     const imports = getImports(raw);
@@ -185,7 +194,10 @@ function runBundleImportRemoveCommand(options) {
     }
     console.log(`bundle import removed: ${alias}`);
 }
-function setBundleImportEnabled(options, enabled) {
+function runBundleImportRemoveCommand(options) {
+    return withBundleImportLock(options.root, () => runBundleImportRemoveCommandLocked(options));
+}
+function setBundleImportEnabledLocked(options, enabled) {
     const alias = normalizeAlias(options.alias);
     const { configPath, raw } = readRawConfig(options.root);
     const imports = getImports(raw);
@@ -206,10 +218,10 @@ function setBundleImportEnabled(options, enabled) {
     console.log(`bundle import ${enabled ? "enabled" : "disabled"}: ${alias}`);
 }
 function runBundleImportEnableCommand(options) {
-    setBundleImportEnabled(options, true);
+    withBundleImportLock(options.root, () => setBundleImportEnabledLocked(options, true));
 }
 function runBundleImportDisableCommand(options) {
-    setBundleImportEnabled(options, false);
+    withBundleImportLock(options.root, () => setBundleImportEnabledLocked(options, false));
 }
 function runBundleImportVerifyCommand(options) {
     const config = (0, config_1.loadConfig)(options.root);

package/dist/commands/checkpoint.js

@@ -13,6 +13,9 @@ const loader_1 = require("../templates/loader");
 const date_1 = require("../util/date");
 const errors_1 = require("../util/errors");
 const id_1 = require("../util/id");
+const atomic_1 = require("../util/atomic");
+const lock_1 = require("../util/lock");
+const sqlite_index_1 = require("../graph/sqlite_index");
 const event_support_1 = require("./event_support");
 function parseCsvList(raw) {
     if (!raw) {
@@ -38,6 +41,9 @@ function normalizeIdRef(value, key) {
     return normalized;
 }
 function nextCheckpointId(index, ws) {
+    return `chk-${maxCheckpointId(index, ws) + 1}`;
+}
+function maxCheckpointId(index, ws) {
     let max = 0;
     for (const node of Object.values(index.nodes)) {
         if (node.ws !== ws) {
@@ -52,7 +58,7 @@ function nextCheckpointId(index, ws) {
             max = parsed;
         }
     }
-    return `chk-${max + 1}`;
+    return max;
 }
 function slugifyTitle(title) {
     const slug = title
@@ -77,7 +83,7 @@ function normalizeWorkspace(value) {
     }
     return normalized;
 }
-function createCheckpoint(options) {
+function createCheckpointLocked(options) {
     const title = options.title.trim();
     if (!title) {
         throw new errors_1.UsageError("checkpoint title cannot be empty");
@@ -99,7 +105,15 @@ function createCheckpoint(options) {
         throw new errors_1.UsageError(`--priority must be between ${priorityMin} and ${priorityMax}`);
     }
     const { index } = (0, index_cache_1.loadIndex)({ root: options.root, config });
-    const id = nextCheckpointId(index, ws);
+    const id = (0, sqlite_index_1.isSqliteBackend)(config)
+        ? (0, sqlite_index_1.reserveSqliteNumericId)({
+            root: options.root,
+            config,
+            ws,
+            prefix: "chk",
+            currentMax: maxCheckpointId(index, ws),
+        }) ?? nextCheckpointId(index, ws)
+        : nextCheckpointId(index, ws);
     const slug = slugifyTitle(title);
     const fileName = `${id}-${slug}.md`;
     const wsEntry = config.workspaces[ws];
@@ -129,8 +143,16 @@ function createCheckpoint(options) {
         relates,
         scope,
     });
-    fs_1.default.mkdirSync(workDir, { recursive: true });
-    fs_1.default.writeFileSync(filePath, content, "utf8");
+    try {
+        (0, atomic_1.writeFileExclusive)(filePath, content);
+    }
+    catch (err) {
+        const code = typeof err === "object" && err !== null && "code" in err ? String(err.code) : "";
+        if (code === "EEXIST") {
+            throw new errors_1.UsageError(`checkpoint file already exists: ${path_1.default.relative(options.root, filePath)}`);
+        }
+        throw err;
+    }
     (0, event_support_1.appendAutomaticEvent)({
         root: options.root,
         ws,
@@ -148,6 +170,10 @@ function createCheckpoint(options) {
         path: path_1.default.relative(options.root, filePath),
     };
 }
+function createCheckpoint(options) {
+    const config = (0, config_1.loadConfig)(options.root);
+    return (0, lock_1.withMutationLock)(options.root, config.index.lock_timeout_ms, () => createCheckpointLocked(options));
+}
 function runCheckpointNewCommand(options) {
     const checkpoint = createCheckpoint(options);
     if (options.json) {

package/dist/commands/doctor.js

@@ -13,31 +13,37 @@ const bundle_imports_1 = require("../graph/bundle_imports");
 const node_1 = require("../graph/node");
 const template_schema_1 = require("../graph/template_schema");
 const visibility_1 = require("../graph/visibility");
+const sqlite_index_1 = require("../graph/sqlite_index");
 const errors_1 = require("../util/errors");
-const REQUIRED_NODE_MAJOR = 18;
+const REQUIRED_NODE_MAJOR = 24;
+const REQUIRED_NODE_MINOR = 15;
 const ARCHIVE_RAW_ALLOWED_DIRS = new Set(["source"]);
-function parseNodeMajor(version) {
-    const major = Number.parseInt(version.split(".")[0] ?? "", 10);
-    if (!Number.isInteger(major)) {
+function parseNodeVersion(version) {
+    const [majorRaw, minorRaw, patchRaw] = version.split(".");
+    const major = Number.parseInt(majorRaw ?? "", 10);
+    const minor = Number.parseInt(minorRaw ?? "", 10);
+    const patch = Number.parseInt(patchRaw ?? "", 10);
+    if (!Number.isInteger(major) || !Number.isInteger(minor) || !Number.isInteger(patch)) {
         return null;
     }
-    return major;
+    return { major, minor, patch };
 }
 function runNodeVersionCheck() {
     const nodeVersion = process.versions.node;
-    const major = parseNodeMajor(nodeVersion);
-    if (major === null) {
+    const parsed = parseNodeVersion(nodeVersion);
+    if (parsed === null) {
         return {
             name: "node-version",
             ok: false,
             detail: `unable to parse Node.js version: ${nodeVersion}`,
         };
     }
-    if (major < REQUIRED_NODE_MAJOR) {
+    if (parsed.major < REQUIRED_NODE_MAJOR ||
+        (parsed.major === REQUIRED_NODE_MAJOR && parsed.minor < REQUIRED_NODE_MINOR)) {
         return {
             name: "node-version",
             ok: false,
-            detail: `Node.js ${nodeVersion} is unsupported (requires >=${REQUIRED_NODE_MAJOR})`,
+            detail: `Node.js ${nodeVersion} is unsupported (requires >=${REQUIRED_NODE_MAJOR}.${REQUIRED_NODE_MINOR}.0)`,
         };
     }
     return {
@@ -46,6 +52,36 @@ function runNodeVersionCheck() {
         detail: `Node.js ${nodeVersion} (ok)`,
     };
 }
+function runSqliteCheck(root, config) {
+    if (!(0, sqlite_index_1.isSqliteBackend)(config)) {
+        return {
+            name: "sqlite-cache",
+            ok: true,
+            detail: "SQLite backend disabled; JSON cache backend active",
+        };
+    }
+    const health = (0, sqlite_index_1.sqliteHealth)(root, config);
+    if (health.errors.length > 0) {
+        return {
+            name: "sqlite-cache",
+            ok: false,
+            detail: health.errors.join("; "),
+        };
+    }
+    if (health.warnings.length > 0) {
+        return {
+            name: "sqlite-cache",
+            ok: true,
+            level: "warn",
+            detail: health.warnings.join("; "),
+        };
+    }
+    return {
+        name: "sqlite-cache",
+        ok: true,
+        detail: `.mdkg SQLite cache ok (${health.size} bytes)`,
+    };
+}
 function walkFiles(root) {
     if (!fs_1.default.existsSync(root)) {
         return [];
@@ -262,6 +298,7 @@ function runDoctorCommand(options) {
         results.push(runArchiveStorageCheck(options.root));
         results.push(runArchiveLargeCacheCheck(options.root, config.archive.large_cache_warning_bytes));
         results.push(runBundleStorageCheck(options.root, config.bundles.output_dir));
+        results.push(runSqliteCheck(options.root, config));
         results.push(...runBundleImportChecks(options.root, config));
         results.push(runVisibilityPolicyCheck(options.root, config, options));
         try {

package/dist/commands/index.js

@@ -6,29 +6,18 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.runIndexCommand = runIndexCommand;
 const path_1 = __importDefault(require("path"));
 const config_1 = require("../core/config");
-const indexer_1 = require("../graph/indexer");
-const index_cache_1 = require("../graph/index_cache");
-const skills_index_cache_1 = require("../graph/skills_index_cache");
-const skills_indexer_1 = require("../graph/skills_indexer");
-const capabilities_indexer_1 = require("../graph/capabilities_indexer");
-const capabilities_index_cache_1 = require("../graph/capabilities_index_cache");
-const bundle_imports_1 = require("../graph/bundle_imports");
+const reindex_1 = require("../graph/reindex");
+const lock_1 = require("../util/lock");
 function runIndexCommand(options) {
     const config = (0, config_1.loadConfig)(options.root);
-    const nodeIndex = (0, indexer_1.buildIndex)(options.root, config, { tolerant: options.tolerant });
-    const skillsIndex = (0, skills_indexer_1.buildSkillsIndex)(options.root, config);
-    const capabilitiesIndex = (0, capabilities_indexer_1.buildCapabilitiesIndex)(options.root, config, nodeIndex);
-    const importsIndex = (0, bundle_imports_1.buildBundleImportsIndex)(options.root, config);
-    const nodesOutputPath = path_1.default.resolve(options.root, config.index.global_index_path);
-    const skillsOutputPath = (0, skills_indexer_1.resolveSkillsIndexPath)(options.root);
-    const capabilitiesOutputPath = (0, capabilities_indexer_1.resolveCapabilitiesIndexPath)(options.root, config);
-    const importsOutputPath = (0, bundle_imports_1.resolveBundleImportsIndexPath)(options.root);
-    (0, index_cache_1.writeIndex)(nodesOutputPath, nodeIndex);
-    (0, skills_index_cache_1.writeSkillsIndex)(skillsOutputPath, skillsIndex);
-    (0, capabilities_index_cache_1.writeCapabilitiesIndex)(capabilitiesOutputPath, capabilitiesIndex);
-    (0, bundle_imports_1.writeBundleImportsIndex)(importsOutputPath, importsIndex.index);
-    console.log(`index written: ${path_1.default.relative(options.root, nodesOutputPath)}`);
-    console.log(`skills index written: ${path_1.default.relative(options.root, skillsOutputPath)}`);
-    console.log(`capabilities index written: ${path_1.default.relative(options.root, capabilitiesOutputPath)}`);
-    console.log(`bundle imports index written: ${path_1.default.relative(options.root, importsOutputPath)}`);
+    (0, lock_1.withMutationLock)(options.root, config.index.lock_timeout_ms, () => {
+        const result = (0, reindex_1.writeDerivedIndexes)(options.root, config, undefined, { tolerant: options.tolerant });
+        console.log(`index written: ${path_1.default.relative(options.root, result.paths.nodes)}`);
+        console.log(`skills index written: ${path_1.default.relative(options.root, result.paths.skills)}`);
+        console.log(`capabilities index written: ${path_1.default.relative(options.root, result.paths.capabilities)}`);
+        console.log(`bundle imports index written: ${path_1.default.relative(options.root, result.paths.imports)}`);
+        if (result.paths.sqlite) {
+            console.log(`sqlite index written: ${path_1.default.relative(options.root, result.paths.sqlite)}`);
+        }
+    });
 }

package/dist/commands/init.js

@@ -409,7 +409,13 @@ function runInitCommand(options) {
     try {
         if (shouldUpdateGitignore) {
             if (appendIgnoreEntries(path_1.default.join(root, ".gitignore"), [
-                ".mdkg/index/",
+                ".mdkg/index/*.json",
+                ".mdkg/index/*.tmp",
+                ".mdkg/index/*.lock",
+                ".mdkg/index/write.lock/",
+                ".mdkg/index/*.sqlite-wal",
+                ".mdkg/index/*.sqlite-shm",
+                ".mdkg/index/*.sqlite-journal",
                 ".mdkg/pack/",
                 ".mdkg/archive/**/source/",
             ])) {

package/dist/commands/new.js

@@ -16,6 +16,10 @@ const date_1 = require("../util/date");
 const errors_1 = require("../util/errors");
 const qid_1 = require("../util/qid");
 const id_1 = require("../util/id");
+const atomic_1 = require("../util/atomic");
+const lock_1 = require("../util/lock");
+const sqlite_index_1 = require("../graph/sqlite_index");
+const reindex_1 = require("../graph/reindex");
 const event_support_1 = require("./event_support");
 const DEC_ID_RE = /^dec-[0-9]+$/;
 const DEC_STATUS = new Set(["proposed", "accepted", "rejected", "superseded"]);
@@ -97,6 +101,9 @@ function slugifyTitle(title) {
     return slug.length > maxLen ? slug.slice(0, maxLen).replace(/-+$/g, "") : slug;
 }
 function nextIdForPrefix(index, ws, prefix) {
+    return `${prefix}-${maxIdForPrefix(index, ws, prefix) + 1}`;
+}
+function maxIdForPrefix(index, ws, prefix) {
     let max = 0;
     const pattern = new RegExp(`^${prefix}-(\\d+)$`);
     for (const node of Object.values(index)) {
@@ -112,7 +119,7 @@ function nextIdForPrefix(index, ws, prefix) {
             max = parsed;
         }
     }
-    return `${prefix}-${max + 1}`;
+    return max;
 }
 function idPrefixForType(type) {
     if (type === "checkpoint") {
@@ -150,7 +157,7 @@ function ensureExists(index, value, ws, label) {
         throw new errors_1.NotFoundError((0, qid_1.formatResolveError)(label, value, resolved, ws));
     }
 }
-function runNewCommand(options) {
+function runNewCommandLocked(options) {
     const title = options.title.trim();
     if (!title) {
         throw new errors_1.UsageError("title cannot be empty");
@@ -181,7 +188,15 @@ function runNewCommand(options) {
     const prefix = idPrefixForType(type);
     const id = options.id !== undefined
         ? normalizeAgentFileId(options.id)
-        : nextIdForPrefix(index.nodes, ws, prefix);
+        : (0, sqlite_index_1.isSqliteBackend)(config)
+            ? (0, sqlite_index_1.reserveSqliteNumericId)({
+                root: options.root,
+                config,
+                ws,
+                prefix,
+                currentMax: maxIdForPrefix(index.nodes, ws, prefix),
+            }) ?? nextIdForPrefix(index.nodes, ws, prefix)
+            : nextIdForPrefix(index.nodes, ws, prefix);
     if (index.nodes[`${ws}:${id}`]) {
         throw new errors_1.UsageError(`node already exists: ${ws}:${id}`);
     }
@@ -317,12 +332,19 @@ function runNewCommand(options) {
         created: today,
         updated: today,
     });
-    fs_1.default.mkdirSync(path_1.default.dirname(filePath), { recursive: true });
-    fs_1.default.writeFileSync(filePath, content, "utf8");
+    try {
+        (0, atomic_1.writeFileExclusive)(filePath, content);
+    }
+    catch (err) {
+        const code = typeof err === "object" && err !== null && "code" in err ? String(err.code) : "";
+        if (code === "EEXIST") {
+            throw new errors_1.UsageError(`node already exists: ${path_1.default.relative(options.root, filePath)}`);
+        }
+        throw err;
+    }
     if (config.index.auto_reindex && !noReindex) {
         const updatedIndex = (0, indexer_1.buildIndex)(options.root, config, { tolerant: config.index.tolerant });
-        const outputPath = path_1.default.resolve(options.root, config.index.global_index_path);
-        (0, index_cache_1.writeIndex)(outputPath, updatedIndex);
+        (0, reindex_1.writeDerivedIndexes)(options.root, config, updatedIndex);
     }
     (0, event_support_1.appendAutomaticEvent)({
         root: options.root,
@@ -354,3 +376,7 @@ function runNewCommand(options) {
     }
     console.log(`node created: ${receipt.qid} (${receipt.path})`);
 }
+function runNewCommand(options) {
+    const config = (0, config_1.loadConfig)(options.root);
+    return (0, lock_1.withMutationLock)(options.root, config.index.lock_timeout_ms, () => runNewCommandLocked(options));
+}