@gramatr/mcp 0.13.74 → 0.13.76

package/dist/bin/brain.d.ts

@@ -81,6 +81,8 @@ export interface ParsedArgs {
     metadata: string[];
     tags?: string;
     onDuplicate?: string;
+    manifest?: string;
+    resume?: string;
 }
 export declare function parseUploadArgs(args: string[]): ParsedArgs;
 export interface ValidatedConfig {
@@ -111,6 +113,19 @@ export interface UploadFileOptions {
     entityId?: string;
     entityName?: string;
     config: ValidatedConfig;
+    /**
+     * Pre-read file bytes. When provided, `uploadFile` will not re-read the file
+     * from disk — the caller (e.g. the resume/manifest loop) has already loaded
+     * and hashed it. Saves one filesystem round-trip per file in batch mode.
+     */
+    prereadBuffer?: Buffer;
+    /**
+     * Batch correlation id (epic #1904 PR 6). The runBrain entry point mints
+     * one UUID per invocation and passes it on every per-file `bulk_upload`
+     * call so audit rows correlate. When omitted, the server mints one per
+     * call (which would prevent correlation across files in the same batch).
+     */
+    batchId?: string;
 }
 export interface UploadResult {
     file: string;

package/dist/bin/brain.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"brain.d.ts","sourceRoot":"","sources":["../../src/bin/brain.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AAyBH,eAAO,MAAM,oBAAoB,aAAoD,CAAC;AAItF;;;;;;;GAOG;AACH,wBAAsB,WAAW,CAC/B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAoBxB;AAID;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAIzD;AAID;;;;GAIG;AACH,eAAO,MAAM,0BAA0B,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAc7D,CAAC;AAIF;;;GAGG;AACH,wBAAgB,uBAAuB,CACrC,MAAM,EAAE,MAAM,EACd,IAAI,CAAC,EAAE;IAAE,SAAS,CAAC,EAAE,MAAM,CAAA;CAAE,GAC5B,MAAM,CAOR;AA2BD,MAAM,WAAW,UAAU;IACzB,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,eAAe,EAAE,OAAO,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,UAAU,CAmD1D;AAID,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC;IAC1C,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,OAAO,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,WAAW,EAAE,MAAM,GAAG,OAAO,GAAG,aAAa,CAAC;CAC/C;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,KAAK,CAAC;IACV,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,IAAI,CAAC;IACT,MAAM,EAAE,eAAe,CAAC;CACzB;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,UAAU,GAAG,iBAAiB,GAAG,iBAAiB,CAoF9F;AAID,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,eAAe,CAAC;IACxB;;;;OAIG;IACH,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB;;;;;OAKG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,mEAAmE;IACnE,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,iBAAiB,GACzB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAqBzB;AAoBD;;GAEG;AACH,wBAAsB,UAAU,CAC9B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,iBAAiB,GACzB,OAAO,CAAC,YAAY,CAAC,CA6DvB;AAID;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,OAAO,GAAG,MAAM,EAAE,CAqBtE;AA+ED;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAsS9D"}

package/dist/bin/brain.js

@@ -37,9 +37,13 @@
  * every CLI upload returns `av_unconfigured` from the server. This is
  * intentional fail-closed behaviour. There is no client-side bypass.
  */
+import { randomUUID } from 'node:crypto';
 import { readFileSync, readdirSync, statSync } from 'node:fs';
 import { extname, basename, join, resolve } from 'node:path';
 import { callTool } from '../proxy/local-client.js';
+import { MANIFEST_SCHEMA, MANIFEST_SCHEMA_V1, decideResume, fileExists, indexManifestByPath, readManifest, sha256Hex, writeManifestAtomic, } from './upload-manifest.js';
+// CLI version stamped into manifests. Synced with @gramatr/mcp package.json.
+const CLI_VERSION = '0.13.76';
 // ── Supported extensions ────────────────────────────────────────────────────
 export const SUPPORTED_EXTENSIONS = new Set(['.txt', '.md', '.csv', '.pdf', '.docx']);
 // ── Text extraction (kept for backwards-compatibility tests) ────────────────
@@ -124,6 +128,8 @@ const VALUE_FLAGS = new Set([
     '--metadata',
     '--tags',
     '--on-duplicate',
+    '--manifest',
+    '--resume',
 ]);
 // Repeatable flags — collect every occurrence into an array.
 const REPEATABLE_FLAGS = new Set(['--metadata']);
@@ -183,6 +189,12 @@ export function parseUploadArgs(args) {
                 case '--on-duplicate':
                     out.onDuplicate = v;
                     break;
+                case '--manifest':
+                    out.manifest = v;
+                    break;
+                case '--resume':
+                    out.resume = v;
+                    break;
             }
             i += 2;
             continue;
@@ -330,6 +342,8 @@ export function buildBulkUploadInput(filePath, buffer, options) {
         input.metadata = options.config.metadata;
     if (options.config.tags.length > 0)
         input.tags = options.config.tags;
+    if (options.batchId)
+        input.batch_id = options.batchId;
     return input;
 }
 function parseToolBody(text) {
@@ -350,13 +364,18 @@ export async function uploadFile(filePath, options) {
         return { file: filePath, skipped: true };
     }
     let buffer;
-    try {
-        buffer = readFileSync(filePath);
+    if (options.prereadBuffer) {
+        buffer = options.prereadBuffer;
     }
-    catch (err) {
-        const message = err instanceof Error ? err.message : String(err);
-        process.stderr.write(`[gramatr] ✗ ${filePath}: ${message}\n`);
-        return { file: filePath, error: message };
+    else {
+        try {
+            buffer = readFileSync(filePath);
+        }
+        catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            process.stderr.write(`[gramatr] ✗ ${filePath}: ${message}\n`);
+            return { file: filePath, error: message };
+        }
     }
     if (buffer.length === 0) {
         process.stderr.write(`[gramatr] skipping ${filePath} (empty content)\n`);
@@ -455,6 +474,16 @@ function printBrainHelp() {
                                 reuse       — append observation to existing entity
                                 new-version — create "<name> v2" / v3 / ...
 
+  Resume / manifest:
+    --manifest <path>         Write a JSON manifest of upload outcomes to <path>,
+                              atomically updated after each file. Schema:
+                              gmtr.upload-manifest.v1 (see docs).
+    --resume <path>           Read a prior manifest and skip files that completed
+                              last run (per content hash). Files with status=error
+                              are retried; files whose content has changed are
+                              re-uploaded. Files no longer on disk are recorded
+                              as skipped (file_missing).
+
   Other flags:
     --dry-run                 Preflight only — show what would be uploaded
     --recursive               With --dir, walk subdirectories
@@ -472,6 +501,8 @@ function printBrainHelp() {
     brain upload --dir ./docs --scope team --team-id <team-uuid>
     brain upload --dir ./research --recursive --metadata source=arxiv --metadata year=2026
     brain upload report.pdf --public
+    brain upload --dir ./docs --manifest /tmp/upload.json
+    brain upload --dir ./docs --manifest /tmp/upload.json --resume /tmp/upload.json
 
   NOTE: bulk_upload requires ClamAV to be deployed on the server. Until then,
         every upload returns av_unconfigured (fail-closed by design).
@@ -546,22 +577,209 @@ export async function runBrain(args) {
         process.stderr.write('[gramatr] dry-run complete — no changes written\n');
         return 0;
     }
+    // ── Manifest + resume setup ────────────────────────────────────────────────
+    // The manifest is the durable record of this run's outcomes. `--resume`
+    // loads a prior manifest so unchanged files can be skipped without a
+    // network call (the O(changed) win); `--manifest` writes after each file
+    // so a crash mid-batch leaves a recoverable partial.
+    //
+    // PR 6 (epic #1904) — batch correlation:
+    //   • A v2 resume manifest already carries a `batch_id`; we reuse it so
+    //     the resumed batch has the same identity as the original.
+    //   • A v1 resume manifest has none; `readManifest` mints one + WARNs.
+    //   • No --resume: mint a fresh UUID for this run.
+    let priorIndex;
+    let priorManifest;
+    if (parsed.resume) {
+        try {
+            priorManifest = readManifest(parsed.resume);
+            priorIndex = indexManifestByPath(priorManifest);
+            process.stderr.write(`[gramatr] resume — loaded ${priorManifest.files.length} prior entr${priorManifest.files.length === 1 ? 'y' : 'ies'} from ${parsed.resume}\n`);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            process.stderr.write(`[gramatr] ✗ Cannot read --resume manifest ${parsed.resume}: ${msg}\n`);
+            return 1;
+        }
+    }
+    const batchId = priorManifest?.batch_id ?? randomUUID();
+    if (priorManifest && !priorManifest.batch_id) {
+        // Defensive — readManifest always backfills v1, but if a future caller
+        // builds a v2 object without batch_id, surface it here too.
+        process.stderr.write(`[gramatr] ⚠ resumed manifest had no batch_id — assigned ${batchId}\n`);
+    }
+    process.stderr.write(`[gramatr] batch_id ${batchId}\n`);
     const options = {
         entityId: parsed.entityId,
         entityName: parsed.entityName,
         config,
+        batchId,
+    };
+    // Seed the in-memory manifest with prior entries — we re-emit them so the
+    // output manifest is a complete record of the union of runs. Always written
+    // as v2 (batch_id required) regardless of the prior manifest's schema.
+    void MANIFEST_SCHEMA_V1; // referenced by tests + read path; keep import live.
+    const manifest = {
+        schema: MANIFEST_SCHEMA,
+        version: CLI_VERSION,
+        started_at: new Date().toISOString(),
+        finished_at: null,
+        scope: {
+            scope: config.scope,
+            ...(config.teamId ? { team_id: config.teamId } : {}),
+            ...(config.orgId ? { org_id: config.orgId } : {}),
+            ...(config.projectId ? { project_id: config.projectId } : {}),
+        },
+        files: [],
+        batch_id: batchId,
+    };
+    // Maintain a path → index map so we can upsert entries in O(1).
+    const fileIndex = new Map();
+    if (priorIndex) {
+        for (const [p, entry] of priorIndex) {
+            fileIndex.set(p, manifest.files.length);
+            manifest.files.push(entry);
+        }
+    }
+    const upsertEntry = (entry) => {
+        const idx = fileIndex.get(entry.path);
+        if (idx === undefined) {
+            fileIndex.set(entry.path, manifest.files.length);
+            manifest.files.push(entry);
+        }
+        else {
+            manifest.files[idx] = entry;
+        }
+    };
+    const flushManifest = () => {
+        if (!parsed.manifest)
+            return;
+        try {
+            writeManifestAtomic(parsed.manifest, manifest);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            process.stderr.write(`[gramatr] ⚠ failed to write manifest ${parsed.manifest}: ${msg}\n`);
+        }
     };
     let hasError = false;
     let hasValidationReject = false;
     for (const filePath of filePaths) {
-        const result = await uploadFile(filePath, options);
+        // Hash the file (or detect missing) before deciding to upload — this is
+        // the O(changed) check that makes resume cheap.
+        let buffer = null;
+        let currentSha = null;
+        let size = 0;
+        let readError = null;
+        if (fileExists(filePath)) {
+            try {
+                buffer = readFileSync(filePath);
+                currentSha = sha256Hex(buffer);
+                size = buffer.length;
+            }
+            catch (err) {
+                // Capture so we can record an error entry without invoking the server.
+                readError = err instanceof Error ? err.message : String(err);
+            }
+        }
+        if (readError !== null) {
+            process.stderr.write(`[gramatr] ✗ ${filePath}: ${readError}\n`);
+            upsertEntry({
+                path: filePath,
+                sha256: '',
+                size: 0,
+                status: 'error',
+                entity_id: null,
+                scan_result: null,
+                reason: readError,
+                completed_at: new Date().toISOString(),
+                batch_id: batchId,
+            });
+            flushManifest();
+            hasError = true;
+            continue;
+        }
+        const decision = decideResume(filePath, currentSha, priorIndex?.get(filePath));
+        if (decision.kind === 'skip-missing') {
+            process.stderr.write(`[gramatr] ↷ ${basename(filePath)}: ${decision.note}\n`);
+            upsertEntry({
+                path: filePath,
+                sha256: '',
+                size: 0,
+                status: 'skipped',
+                entity_id: null,
+                scan_result: null,
+                reason: 'file_missing',
+                completed_at: new Date().toISOString(),
+                batch_id: batchId,
+            });
+            flushManifest();
+            continue;
+        }
+        if (decision.kind === 'skip-previous') {
+            process.stderr.write(`[gramatr] ↷ ${basename(filePath)}: ${decision.note}\n`);
+            // Refresh completed_at so the manifest reflects this run's pass.
+            // Skipped via prior manifest — preserve the prior batch_id if it had
+            // one (so the original group identity survives), otherwise stamp with
+            // the current run's batchId so all entries in the v2 manifest carry one.
+            upsertEntry({
+                ...decision.entry,
+                completed_at: new Date().toISOString(),
+                batch_id: decision.entry.batch_id ?? batchId,
+            });
+            flushManifest();
+            // Previously-rejected files do NOT bump this run's exit code — we are
+            // not re-attempting them, so they are not "this run's" failures.
+            continue;
+        }
+        // ── Actually upload ────────────────────────────────────────────────────
+        const result = await uploadFile(filePath, buffer ? { ...options, prereadBuffer: buffer } : options);
+        let status;
+        let entityId = result.entityId ?? null;
+        let scanResult = null;
+        let reason = null;
         if (result.validationReason) {
+            status = 'rejected';
+            reason = result.validationReason;
             hasValidationReject = true;
         }
         else if (result.error) {
+            status = 'error';
+            reason = result.error;
             hasError = true;
         }
-    }
+        else if (result.skipped) {
+            // Empty file or unsupported extension — recorded as skipped without a
+            // server entity_id.
+            status = 'skipped';
+            reason = 'unsupported_or_empty';
+        }
+        else if (result.wasDuplicate) {
+            // on_duplicate=reuse path — server attached observation to existing entity.
+            // For on_duplicate=skip the server returns was_duplicate=true with no new
+            // observation, which is captured here as 'skipped'.
+            status = config.onDuplicate === 'skip' ? 'skipped' : 'reused';
+            scanResult = 'clean';
+        }
+        else {
+            status = 'uploaded';
+            scanResult = 'clean';
+        }
+        upsertEntry({
+            path: filePath,
+            sha256: currentSha || '',
+            size,
+            status,
+            entity_id: entityId,
+            scan_result: scanResult,
+            reason,
+            completed_at: new Date().toISOString(),
+            batch_id: batchId,
+        });
+        flushManifest();
+    }
+    manifest.finished_at = new Date().toISOString();
+    flushManifest();
     // Validator rejection takes precedence — distinct exit code so scripts can
     // differentiate "server said no" from "transport blew up".
     if (hasValidationReject)

package/dist/bin/brain.js.map

@@ -1 +1 @@
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package/dist/bin/upload-manifest.d.ts

@@ -0,0 +1,141 @@
+/**
+ * upload-manifest — JSON manifest schema + atomic IO for `gramatr brain upload`.
+ *
+ * Epic #1904 PR 5. Records the outcome of every file in a bulk upload run so
+ * that:
+ *   - a crashed batch can be resumed without re-uploading completed files
+ *   - unchanged files can be skipped without a network round-trip
+ *   - the operator has a full audit trail (entity_id, scan_result, reason)
+ *
+ * The manifest is single-writer (the CLI process). No locking. Atomic writes
+ * are achieved by writing `<path>.tmp` then renaming over the target — POSIX
+ * `rename(2)` is atomic on the same filesystem.
+ *
+ * `finished_at` is null until the run completes. A crashed run leaves it null,
+ * which is the signal `--resume` uses to confirm there is recoverable state.
+ */
+/**
+ * Current manifest schema. v2 (epic #1904 PR 6) adds the top-level + per-entry
+ * `batch_id` correlation field so a manifest is unambiguously tied to a single
+ * uploaded batch in the dashboard's history view.
+ *
+ * v1 manifests remain readable for backwards compat — `parseManifest`
+ * accepts either schema string and `readManifest` will up-convert v1 →
+ * v2-shaped object in memory by minting a fresh `batch_id` and emitting a
+ * one-line WARN to stderr (caller sees the new identity is synthetic).
+ */
+export declare const MANIFEST_SCHEMA = "gmtr.upload-manifest.v2";
+export declare const MANIFEST_SCHEMA_V1 = "gmtr.upload-manifest.v1";
+export type ManifestEntryStatus = 'uploaded' | 'reused' | 'skipped' | 'rejected' | 'error';
+export interface UploadManifestEntry {
+    /** Absolute path on the uploader's filesystem at the time of the run. */
+    path: string;
+    /** Hex sha256 of the file's bytes at the time of the run. */
+    sha256: string;
+    /** File size in bytes. */
+    size: number;
+    /** Outcome — see ManifestEntryStatus. */
+    status: ManifestEntryStatus;
+    /** Server entity_id for uploaded/reused/skipped; null otherwise. */
+    entity_id: string | null;
+    /** Server scan_result (e.g. "clean", "infected", "unconfigured"); null when unknown. */
+    scan_result: string | null;
+    /**
+     * For status=rejected: the UploadValidationError reason.
+     * For status=error: the error message.
+     * For status=skipped via missing-file: "file_missing".
+     * Otherwise null.
+     */
+    reason: string | null;
+    /** ISO-8601 timestamp of when this file's processing completed. */
+    completed_at: string;
+    /**
+     * Batch correlation id (v2). Mirrors the manifest's top-level `batch_id`
+     * for redundancy + cross-validation. Always present in v2; absent on
+     * entries inherited verbatim from a legacy v1 manifest until they are
+     * rewritten.
+     */
+    batch_id?: string;
+}
+export interface UploadManifestScope {
+    scope: 'user' | 'team' | 'org' | 'public';
+    team_id?: string;
+    org_id?: string;
+    project_id?: string;
+}
+export interface UploadManifest {
+    schema: typeof MANIFEST_SCHEMA | typeof MANIFEST_SCHEMA_V1;
+    version: string;
+    started_at: string;
+    finished_at: string | null;
+    scope: UploadManifestScope;
+    files: UploadManifestEntry[];
+    /**
+     * Batch correlation id. Required in v2; on a v1 manifest read via
+     * `readManifest`, this is back-filled with a freshly minted UUID and a
+     * WARN is logged to stderr so callers see the identity is synthetic.
+     */
+    batch_id?: string;
+}
+/**
+ * Domain-specific error thrown by the manifest parser. Distinct from generic
+ * `Error` so callers (and rubric dimension B1) can identify it precisely.
+ */
+export declare class ManifestSchemaError extends Error {
+    constructor(message: string);
+}
+/**
+ * Compute the hex sha256 digest of a buffer. Stable across runs and platforms.
+ */
+export declare function sha256Hex(buffer: Buffer): string;
+/**
+ * Validate that an arbitrary value matches the gmtr.upload-manifest.v1 schema.
+ * Returns the manifest typed if valid, throws Error with a specific message
+ * otherwise. Forgiving on unknown fields (forward-compat) but strict on the
+ * required ones.
+ */
+export declare function parseManifest(value: unknown): UploadManifest;
+/**
+ * Write the manifest to `path` atomically:
+ *   1. Serialize JSON
+ *   2. Write to `<path>.tmp`
+ *   3. fs.renameSync into place (POSIX-atomic on same filesystem)
+ *
+ * A reader observing `path` will always see either the previous full contents
+ * or the new full contents — never a partially-written file.
+ */
+export declare function writeManifestAtomic(path: string, manifest: UploadManifest): void;
+/**
+ * Read and validate a manifest from disk. Throws if the file does not exist
+ * or fails schema validation.
+ */
+export declare function readManifest(path: string): UploadManifest;
+/**
+ * Build a Map<absolutePath, entry> from a manifest's files array. Last entry
+ * wins (the manifest is append/upsert per file, so duplicates should not occur,
+ * but be defensive).
+ */
+export declare function indexManifestByPath(manifest: UploadManifest): Map<string, UploadManifestEntry>;
+export type ResumeDecision = {
+    kind: 'upload';
+} | {
+    kind: 'skip-previous';
+    entry: UploadManifestEntry;
+    note: string;
+} | {
+    kind: 'skip-missing';
+    note: string;
+};
+/**
+ * Decide what to do with a file given the resume manifest's record (if any).
+ *
+ * - Not in manifest                              → upload
+ * - Path no longer exists on disk                → skip-missing
+ * - In manifest, status=error                    → upload (retry)
+ * - In manifest, hash differs from current bytes → upload (re-upload)
+ * - In manifest, hash matches, status terminal   → skip-previous
+ */
+export declare function decideResume(filePath: string, currentSha256: string | null, prior: UploadManifestEntry | undefined): ResumeDecision;
+/** True iff a file currently exists at the given path. */
+export declare function fileExists(path: string): boolean;
+//# sourceMappingURL=upload-manifest.d.ts.map

package/dist/bin/upload-manifest.d.ts.map

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package/dist/bin/upload-manifest.js

@@ -0,0 +1,222 @@
+/**
+ * upload-manifest — JSON manifest schema + atomic IO for `gramatr brain upload`.
+ *
+ * Epic #1904 PR 5. Records the outcome of every file in a bulk upload run so
+ * that:
+ *   - a crashed batch can be resumed without re-uploading completed files
+ *   - unchanged files can be skipped without a network round-trip
+ *   - the operator has a full audit trail (entity_id, scan_result, reason)
+ *
+ * The manifest is single-writer (the CLI process). No locking. Atomic writes
+ * are achieved by writing `<path>.tmp` then renaming over the target — POSIX
+ * `rename(2)` is atomic on the same filesystem.
+ *
+ * `finished_at` is null until the run completes. A crashed run leaves it null,
+ * which is the signal `--resume` uses to confirm there is recoverable state.
+ */
+import { createHash, randomUUID } from 'node:crypto';
+import { existsSync, readFileSync, renameSync, writeFileSync } from 'node:fs';
+/**
+ * Current manifest schema. v2 (epic #1904 PR 6) adds the top-level + per-entry
+ * `batch_id` correlation field so a manifest is unambiguously tied to a single
+ * uploaded batch in the dashboard's history view.
+ *
+ * v1 manifests remain readable for backwards compat — `parseManifest`
+ * accepts either schema string and `readManifest` will up-convert v1 →
+ * v2-shaped object in memory by minting a fresh `batch_id` and emitting a
+ * one-line WARN to stderr (caller sees the new identity is synthetic).
+ */
+export const MANIFEST_SCHEMA = 'gmtr.upload-manifest.v2';
+export const MANIFEST_SCHEMA_V1 = 'gmtr.upload-manifest.v1';
+// ── Errors ──────────────────────────────────────────────────────────────────
+/**
+ * Domain-specific error thrown by the manifest parser. Distinct from generic
+ * `Error` so callers (and rubric dimension B1) can identify it precisely.
+ */
+export class ManifestSchemaError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'ManifestSchemaError';
+    }
+}
+// ── sha256 ──────────────────────────────────────────────────────────────────
+/**
+ * Compute the hex sha256 digest of a buffer. Stable across runs and platforms.
+ */
+export function sha256Hex(buffer) {
+    return createHash('sha256').update(buffer).digest('hex');
+}
+// ── Schema validation ───────────────────────────────────────────────────────
+const VALID_STATUSES = new Set([
+    'uploaded',
+    'reused',
+    'skipped',
+    'rejected',
+    'error',
+]);
+const VALID_SCOPES = new Set(['user', 'team', 'org', 'public']);
+/**
+ * Validate that an arbitrary value matches the gmtr.upload-manifest.v1 schema.
+ * Returns the manifest typed if valid, throws Error with a specific message
+ * otherwise. Forgiving on unknown fields (forward-compat) but strict on the
+ * required ones.
+ */
+export function parseManifest(value) {
+    if (typeof value !== 'object' || value === null) {
+        throw new ManifestSchemaError('manifest must be a JSON object');
+    }
+    const obj = value;
+    if (obj.schema !== MANIFEST_SCHEMA && obj.schema !== MANIFEST_SCHEMA_V1) {
+        throw new ManifestSchemaError(`manifest.schema must be "${MANIFEST_SCHEMA}" or "${MANIFEST_SCHEMA_V1}", got ${JSON.stringify(obj.schema)}`);
+    }
+    // v2 requires top-level batch_id. v1 may omit it (we backfill on read).
+    if (obj.schema === MANIFEST_SCHEMA && typeof obj.batch_id !== 'string') {
+        throw new ManifestSchemaError('manifest.batch_id must be a string (required in v2)');
+    }
+    if (typeof obj.version !== 'string') {
+        throw new ManifestSchemaError('manifest.version must be a string');
+    }
+    if (typeof obj.started_at !== 'string') {
+        throw new ManifestSchemaError('manifest.started_at must be a string');
+    }
+    if (obj.finished_at !== null && typeof obj.finished_at !== 'string') {
+        throw new ManifestSchemaError('manifest.finished_at must be a string or null');
+    }
+    if (typeof obj.scope !== 'object' || obj.scope === null) {
+        throw new ManifestSchemaError('manifest.scope must be an object');
+    }
+    const scope = obj.scope;
+    if (typeof scope.scope !== 'string' || !VALID_SCOPES.has(scope.scope)) {
+        throw new ManifestSchemaError(`manifest.scope.scope must be one of user|team|org|public`);
+    }
+    if (!Array.isArray(obj.files)) {
+        throw new ManifestSchemaError('manifest.files must be an array');
+    }
+    for (let i = 0; i < obj.files.length; i++) {
+        const e = obj.files[i];
+        if (typeof e !== 'object' || e === null) {
+            throw new ManifestSchemaError(`manifest.files[${i}] must be an object`);
+        }
+        for (const k of ['path', 'sha256', 'completed_at']) {
+            if (typeof e[k] !== 'string') {
+                throw new ManifestSchemaError(`manifest.files[${i}].${k} must be a string`);
+            }
+        }
+        if (typeof e.size !== 'number') {
+            throw new ManifestSchemaError(`manifest.files[${i}].size must be a number`);
+        }
+        if (typeof e.status !== 'string' || !VALID_STATUSES.has(e.status)) {
+            throw new ManifestSchemaError(`manifest.files[${i}].status must be one of ${[...VALID_STATUSES].join('|')}`);
+        }
+        if (e.entity_id !== null && typeof e.entity_id !== 'string') {
+            throw new ManifestSchemaError(`manifest.files[${i}].entity_id must be a string or null`);
+        }
+        if (e.scan_result !== null && typeof e.scan_result !== 'string') {
+            throw new ManifestSchemaError(`manifest.files[${i}].scan_result must be a string or null`);
+        }
+        if (e.reason !== null && typeof e.reason !== 'string') {
+            throw new ManifestSchemaError(`manifest.files[${i}].reason must be a string or null`);
+        }
+    }
+    return value;
+}
+// ── Atomic IO ───────────────────────────────────────────────────────────────
+/**
+ * Write the manifest to `path` atomically:
+ *   1. Serialize JSON
+ *   2. Write to `<path>.tmp`
+ *   3. fs.renameSync into place (POSIX-atomic on same filesystem)
+ *
+ * A reader observing `path` will always see either the previous full contents
+ * or the new full contents — never a partially-written file.
+ */
+export function writeManifestAtomic(path, manifest) {
+    const tmp = `${path}.tmp`;
+    writeFileSync(tmp, JSON.stringify(manifest, null, 2), 'utf8');
+    renameSync(tmp, path);
+}
+/**
+ * Read and validate a manifest from disk. Throws if the file does not exist
+ * or fails schema validation.
+ */
+export function readManifest(path) {
+    const raw = readFileSync(path, 'utf8');
+    let parsed;
+    try {
+        parsed = JSON.parse(raw);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        throw new ManifestSchemaError(`manifest at ${path} is not valid JSON: ${msg}`);
+    }
+    const m = parseManifest(parsed);
+    // v1 backwards-compat: mint a fresh batch_id so the rest of the pipeline can
+    // assume it exists. WARN so the caller knows the identity differs from the
+    // original run.
+    if (m.schema === MANIFEST_SCHEMA_V1 && !m.batch_id) {
+        const newId = randomUUID();
+        process.stderr.write(`[gramatr] ⚠ manifest at ${path} is v1 (no batch_id); assigning fresh batch_id ${newId} — resumed batch identity differs from the original\n`);
+        return { ...m, batch_id: newId };
+    }
+    return m;
+}
+// ── Resume index ────────────────────────────────────────────────────────────
+/**
+ * Build a Map<absolutePath, entry> from a manifest's files array. Last entry
+ * wins (the manifest is append/upsert per file, so duplicates should not occur,
+ * but be defensive).
+ */
+export function indexManifestByPath(manifest) {
+    const map = new Map();
+    for (const e of manifest.files)
+        map.set(e.path, e);
+    return map;
+}
+/**
+ * Decide what to do with a file given the resume manifest's record (if any).
+ *
+ * - Not in manifest                              → upload
+ * - Path no longer exists on disk                → skip-missing
+ * - In manifest, status=error                    → upload (retry)
+ * - In manifest, hash differs from current bytes → upload (re-upload)
+ * - In manifest, hash matches, status terminal   → skip-previous
+ */
+export function decideResume(filePath, currentSha256, prior) {
+    if (currentSha256 === null) {
+        return {
+            kind: 'skip-missing',
+            note: 'file removed since last run',
+        };
+    }
+    if (!prior)
+        return { kind: 'upload' };
+    if (prior.status === 'error')
+        return { kind: 'upload' };
+    if (prior.sha256 !== currentSha256)
+        return { kind: 'upload' };
+    // Terminal statuses with matching hash — safe to skip.
+    let note;
+    switch (prior.status) {
+        case 'uploaded':
+            note = `previously uploaded as entity ${prior.entity_id ?? 'unknown'}`;
+            break;
+        case 'reused':
+            note = `previously reused entity ${prior.entity_id ?? 'unknown'}`;
+            break;
+        case 'skipped':
+            note = `previously skipped (entity ${prior.entity_id ?? 'unknown'})`;
+            break;
+        case 'rejected':
+            note = `previously rejected: ${prior.reason ?? 'unknown'}`;
+            break;
+        default:
+            note = `previously ${prior.status}`;
+    }
+    return { kind: 'skip-previous', entry: prior, note };
+}
+// ── Helpers ─────────────────────────────────────────────────────────────────
+/** True iff a file currently exists at the given path. */
+export function fileExists(path) {
+    return existsSync(path);
+}
+//# sourceMappingURL=upload-manifest.js.map

package/dist/bin/upload-manifest.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gramatr/mcp",
-  "version": "0.13.74",
+  "version": "0.13.76",
   "description": "grāmatr — Intelligence middleware for AI agents. Pre-classifies every request, injects relevant memory and behavioral context, enforces data quality, and maintains session continuity across Claude, ChatGPT, Codex, Cursor, Gemini, and any MCP-compatible client.",
   "license": "SEE LICENSE IN LICENSE",
   "publishConfig": {