@eir-labs/coltrane 0.24.13 → 0.24.14

package/dist/src/cli.d.ts

@@ -31,7 +31,7 @@ export interface CliIO {
     /** Injected for tests. Production reads stdin for `--input -`. */
     stdin?: () => string;
 }
-export declare const USAGE = "coltrane 0.24.13\n\n  coltrane validate                     load the genome; exit non-zero on load errors OR on an\n                                        orphan \u2014 a standards/|domain_types/|agents/ file with no\n                                        genome_mutation seal in the tracked genome ledger\n  coltrane dispatch <standard>          run a standard\n  coltrane monitor <gig-id>             report a gig's progress\n  coltrane logs <gig-id>                per-chair logs for a gig\n  coltrane abort <gig-id>               stop a running gig\n  coltrane trace <output-id>            walk an output's provenance\n  coltrane simulate <standard>          cost/shape a standard without running it\n  coltrane health                       engine + store health\n  coltrane serve                        run the MCP server on stdio\n  coltrane enqueue <standard>           queue a gig on the LOCAL file queue (no store, no key)\n                                        (env: COLTRANE_QUEUE_DIR \u2014 its absence is the whole\n                                         difference between local and hosted)\n  coltrane work                         claim one queued gig from the org store and run it\n  coltrane work --check                  report whether this box's drain environment is configured\n                                        and exit without claiming (0 ready, 1 not ready)\n                                        (env: COLTRANE_STORE_URL, COLTRANE_STORE_ANON,\n                                         COLTRANE_AGENT_TOKEN; results drain via\n                                         COLTRANE_DRAIN_URL + COLTRANE_DRAIN_KEY;\n                                         checkpoints under COLTRANE_WORKER_CHECKPOINTS,\n                                         default ~/.coltrane/worker-checkpoints;\n                                         exit 0 complete or parked, 1 failed, 3 queue empty)\n\nOptions\n  --input <json|@file|->                dispatch payload; @file reads a file, - reads stdin\n  --depth <skim|standard|deep>          tighten the per-chair turn cap\n  --budget <dollars>                    per-gig ceiling; the run stops when it is gone\n  --reuse                               allow chair-level reuse of prior sealed outputs\n  --resume <gig-id>                     continue a gig that died mid-pipeline\n  --approve <role>=<json|@file>         a human chair's verdict; repeat once per chair\n  --as <name>                           who is approving; sealed as the verdict's author\n  --wait                                block until the run finishes\n  --follow                              poll until the gig reaches a terminal state\n  --direction <upstream|downstream|both>  for trace\n  --json                                print the raw result to stdout\n  --genome <path>                       genome root (default: $COLTRANE_GENOME or cwd)\n  --help, --version\n\nA dispatch that reaches a chair a HUMAN holds parks: it names the waiting chair and exits 0,\nbecause a gig waiting on a person is not a failed gig. Approve it on the resume \u2014\n\n  coltrane dispatch <standard> --resume <gig> \\\n      --approve approve=@verdict.json --as eugene\n\n--input is NOT required on an approve-only resume: when every remaining chair is human the\ncheckpoint's recorded payload stands and the omission inherits it. If you DO pass --input it is\nchecked against the checkpoint, and a disagreement still refuses the resume.\n";
+export declare const USAGE = "coltrane 0.24.14\n\n  coltrane validate                     load the genome; exit non-zero on load errors OR on an\n                                        orphan \u2014 a standards/|domain_types/|agents/ file with no\n                                        genome_mutation seal in the tracked genome ledger\n  coltrane seal-genome [<genome_dir>]   bulk-seal a pre-sealing genome: append a genome_mutation\n                                        seal for every standards/|domain_types/|agents/ file not yet\n                                        sealed, via the blessed sealDefinition path. Content is\n                                        byte-unchanged; a second run seals nothing already sealed.\n                                        (default genome_dir: cwd)\n  coltrane dispatch <standard>          run a standard\n  coltrane monitor <gig-id>             report a gig's progress\n  coltrane logs <gig-id>                per-chair logs for a gig\n  coltrane abort <gig-id>               stop a running gig\n  coltrane trace <output-id>            walk an output's provenance\n  coltrane simulate <standard>          cost/shape a standard without running it\n  coltrane health                       engine + store health\n  coltrane serve                        run the MCP server on stdio\n  coltrane enqueue <standard>           queue a gig on the LOCAL file queue (no store, no key)\n                                        (env: COLTRANE_QUEUE_DIR \u2014 its absence is the whole\n                                         difference between local and hosted)\n  coltrane work                         claim one queued gig from the org store and run it\n  coltrane work --check                  report whether this box's drain environment is configured\n                                        and exit without claiming (0 ready, 1 not ready)\n                                        (env: COLTRANE_STORE_URL, COLTRANE_STORE_ANON,\n                                         COLTRANE_AGENT_TOKEN; results drain via\n                                         COLTRANE_DRAIN_URL + COLTRANE_DRAIN_KEY;\n                                         checkpoints under COLTRANE_WORKER_CHECKPOINTS,\n                                         default ~/.coltrane/worker-checkpoints;\n                                         exit 0 complete or parked, 1 failed, 3 queue empty)\n\nOptions\n  --input <json|@file|->                dispatch payload; @file reads a file, - reads stdin\n  --depth <skim|standard|deep>          tighten the per-chair turn cap\n  --budget <dollars>                    per-gig ceiling; the run stops when it is gone\n  --reuse                               allow chair-level reuse of prior sealed outputs\n  --resume <gig-id>                     continue a gig that died mid-pipeline\n  --approve <role>=<json|@file>         a human chair's verdict; repeat once per chair\n  --as <name>                           who is approving; sealed as the verdict's author\n  --wait                                block until the run finishes\n  --follow                              poll until the gig reaches a terminal state\n  --direction <upstream|downstream|both>  for trace\n  --json                                print the raw result to stdout\n  --genome <path>                       genome root (default: $COLTRANE_GENOME or cwd)\n  --help, --version\n\nA dispatch that reaches a chair a HUMAN holds parks: it names the waiting chair and exits 0,\nbecause a gig waiting on a person is not a failed gig. Approve it on the resume \u2014\n\n  coltrane dispatch <standard> --resume <gig> \\\n      --approve approve=@verdict.json --as eugene\n\n--input is NOT required on an approve-only resume: when every remaining chair is human the\ncheckpoint's recorded payload stands and the omission inherits it. If you DO pass --input it is\nchecked against the checkpoint, and a disagreement still refuses the resume.\n";
 interface Parsed {
     cmd: string | undefined;
     positional: string[];

package/dist/src/cli.js

@@ -24,6 +24,8 @@
  */
 import { dispatchTool, bootstrapServerDeps } from "./server.js";
 import { detectGenomeOrphans } from "./genome_writer.js";
+import { sealGenome } from "./seal_genome.js";
+import { FileLedger, defaultGenomeLedgerPath } from "./ledger.js";
 import { COLTRANE_VERSION } from "./version.js";
 import { workOnce } from "./worker.js";
 import { openLocalQueue, selectQueueBacking, LOCAL_QUEUE_DIR_VAR } from "./local_queue.js";
@@ -37,6 +39,11 @@ export const USAGE = `coltrane ${COLTRANE_VERSION}
   coltrane validate                     load the genome; exit non-zero on load errors OR on an
                                         orphan — a standards/|domain_types/|agents/ file with no
                                         genome_mutation seal in the tracked genome ledger
+  coltrane seal-genome [<genome_dir>]   bulk-seal a pre-sealing genome: append a genome_mutation
+                                        seal for every standards/|domain_types/|agents/ file not yet
+                                        sealed, via the blessed sealDefinition path. Content is
+                                        byte-unchanged; a second run seals nothing already sealed.
+                                        (default genome_dir: cwd)
   coltrane dispatch <standard>          run a standard
   coltrane monitor <gig-id>             report a gig's progress
   coltrane logs <gig-id>                per-chair logs for a gig
@@ -192,7 +199,7 @@ export async function runCli(argv, io) {
         io.out(USAGE);
         return cmd === undefined ? 2 : 0;
     }
-    const KNOWN = ["validate", "dispatch", "enqueue", "monitor", "logs", "abort", "trace", "simulate", "health", "serve", "work"];
+    const KNOWN = ["validate", "seal-genome", "dispatch", "enqueue", "monitor", "logs", "abort", "trace", "simulate", "health", "serve", "work"];
     if (!KNOWN.includes(cmd)) {
         line(io, `unknown command "${cmd}"\n`);
         io.err(USAGE);
@@ -333,6 +340,30 @@ export async function runCli(argv, io) {
             (res.error ? ` — ${res.error}` : ""));
         return code;
     }
+    // `seal-genome` is the bulk-migration door (WO-F07 Article I). It needs ONLY the genome ledger
+    // and the genome dir — not bootstrapServerDeps, which would load every definition and couple the
+    // command to server init for no benefit. It reuses sealDefinition (the blessed write path), so it
+    // never reimplements sealing; it only iterates it. Exit 0 when every file is sealed-or-skipped,
+    // exit 1 if any file errored — a partial seal leaves detectGenomeOrphans non-empty, so exit 0
+    // would falsely signal a fully-sealed genome (matching the validate exit-code contract).
+    if (cmd === "seal-genome") {
+        const genome_dir = positional[0] ?? process.cwd();
+        let report;
+        try {
+            report = sealGenome(genome_dir, new FileLedger(defaultGenomeLedgerPath(genome_dir)));
+        }
+        catch (e) {
+            line(io, `seal-genome failed: ${e instanceof Error ? e.message : String(e)}`);
+            return 1;
+        }
+        for (const { path, error } of report.errors)
+            line(io, `error  ${path}: ${error}`);
+        if (emitJson(io, json, report))
+            return report.errors.length === 0 ? 0 : 1;
+        line(io, `sealed ${report.sealed.length}, skipped ${report.skipped.length}` +
+            (report.errors.length ? `, ${report.errors.length} error(s)` : ""));
+        return report.errors.length === 0 ? 0 : 1;
+    }
     // Booting loads the genome and constructs the invoker, so it happens only after the command
     // is known to be real — `--help` and a typo must not pay for it or fail inside it.
     let deps;

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package/dist/src/seal_genome.d.ts

@@ -0,0 +1,24 @@
+import type { Ledger } from "./ledger.js";
+/** What the bulk seal did, as genome-relative PATHS (not bare counts). Paths — not counts — so the
+ *  caller can BOTH tally (`.length`) and NAME which file was sealed / skipped / failed: the CLI
+ *  reports counts, and the slug-fold law must assert WHICH file was skipped. Per-file `errors` make
+ *  the loop fault-tolerant — a malformed / non-canonicalisable file is reported without aborting the
+ *  files after it. */
+export interface SealGenomeReport {
+    sealed: string[];
+    skipped: string[];
+    errors: Array<{
+        path: string;
+        error: string;
+    }>;
+}
+/**
+ * Seal every genome file under standards/, domain_types/, agents/ that is not already sealed.
+ *
+ * A file is ALREADY SEALED when some `genome_mutation` entry carries a matching `content_hash` under
+ * a subject_slug that folds to the file's base slug — the same identity `detectGenomeOrphans` reads.
+ * Such files are SKIPPED (idempotent: a second run seals nothing). Otherwise the file's parsed def is
+ * passed through `sealDefinition`, appending one seal keyed by the per-kind event and re-writing the
+ * file byte-identically. Each file is wrapped so a malformed one is reported per-file, not fatal.
+ */
+export declare function sealGenome(genome_dir: string, ledger: Ledger): SealGenomeReport;

package/dist/src/seal_genome.js

@@ -0,0 +1,87 @@
+// WO-F07 Article I — `seal-genome`, the bulk-migration primitive.
+//
+// The WO-F06 orphan invariant (`coltrane validate` fails on a standards/|domain_types/|agents/ file
+// with no `genome_mutation` seal in the git-tracked genome ledger) had no MIGRATION primitive. A
+// pre-sealing genome — every file hand-authored or predating the sealed regime — is all orphans,
+// and there was no command to bring it in-regime in bulk. `sealGenome` is that primitive: it
+// iterates the blessed write path (`sealDefinition`, src/genome_writer.ts:69) over every genome file
+// and, for each file not already sealed, records its `genome_mutation` seal.
+//
+// It seals IDENTITY, it does NOT rewrite content. `sealDefinition` re-serializes the parsed object
+// as `JSON.stringify(def, null, 2) + "\n"`; for a genome already in that on-disk form,
+// `writeGenomeFileVersioned` writes byte-identical content and snapshots no prior version. So a file
+// that was already canonically serialized is byte-unchanged — only the ledger grows.
+import { readdirSync, readFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+import { canonJson, sha256Hex } from "./canonical_form.js";
+import { sealDefinition, ORPHAN_SCAN_SUBDIRS } from "./genome_writer.js";
+/** The `genome_mutation` event each genome kind seals under — the MCP-tool-name convention
+ *  `sealDefinition` already uses (agent_define / standard_compose / type_register). A per-kind event
+ *  (not a single generic "seal_genome") keeps kind provenance in the audit trail. */
+const KIND_EVENT = {
+    standards: "standard_compose",
+    domain_types: "type_register",
+    agents: "agent_define",
+};
+/** Fold `<slug>@v<n>` back to `<slug>` — a version-producing seal (agent_evolve / type_extend)
+ *  records the versioned identity while still materialising the flat `<slug>.json`. IDENTICAL to the
+ *  fold in detectGenomeOrphans (src/genome_writer.ts:260); if it diverged, a versioned-sealed file
+ *  would read as an orphan here and be re-sealed, breaking idempotency. */
+function baseSlug(subject_slug) {
+    return subject_slug.split("@")[0];
+}
+/**
+ * Seal every genome file under standards/, domain_types/, agents/ that is not already sealed.
+ *
+ * A file is ALREADY SEALED when some `genome_mutation` entry carries a matching `content_hash` under
+ * a subject_slug that folds to the file's base slug — the same identity `detectGenomeOrphans` reads.
+ * Such files are SKIPPED (idempotent: a second run seals nothing). Otherwise the file's parsed def is
+ * passed through `sealDefinition`, appending one seal keyed by the per-kind event and re-writing the
+ * file byte-identically. Each file is wrapped so a malformed one is reported per-file, not fatal.
+ */
+export function sealGenome(genome_dir, ledger) {
+    const report = { sealed: [], skipped: [], errors: [] };
+    // The seal index: base slug → the set of content hashes already sealed under it. Queried once —
+    // every file this run seals has a distinct slug, so no in-run entry can shadow a later file.
+    const sealedHashes = new Map();
+    for (const e of ledger.query({ kind: "genome_mutation" })) {
+        const entry = e;
+        if (typeof entry.subject_slug !== "string")
+            continue;
+        const slug = baseSlug(entry.subject_slug);
+        let set = sealedHashes.get(slug);
+        if (!set) {
+            set = new Set();
+            sealedHashes.set(slug, set);
+        }
+        if (typeof entry.content_hash === "string")
+            set.add(entry.content_hash);
+    }
+    for (const subdir of ORPHAN_SCAN_SUBDIRS) {
+        const dir = join(genome_dir, subdir);
+        if (!existsSync(dir))
+            continue;
+        for (const dirent of readdirSync(dir, { withFileTypes: true })) {
+            if (!dirent.isFile() || !dirent.name.endsWith(".json"))
+                continue;
+            const slug = dirent.name.slice(0, -".json".length);
+            const rel = `${subdir}/${dirent.name}`;
+            try {
+                const def = JSON.parse(readFileSync(join(dir, dirent.name), "utf-8"));
+                const content_hash = sha256Hex(canonJson(def));
+                // Already sealed: an entry folding to this base slug carries this exact content hash.
+                if (sealedHashes.get(slug)?.has(content_hash)) {
+                    report.skipped.push(rel);
+                    continue;
+                }
+                sealDefinition(KIND_EVENT[subdir], slug, def, ledger, genome_dir, subdir);
+                report.sealed.push(rel);
+            }
+            catch (e) {
+                report.errors.push({ path: rel, error: e instanceof Error ? e.message : String(e) });
+            }
+        }
+    }
+    return report;
+}
+//# sourceMappingURL=seal_genome.js.map

package/dist/src/seal_genome.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seal_genome.js","sourceRoot":"","sources":["../../src/seal_genome.ts"],"names":[],"mappings":"AAAA,kEAAkE;AAClE,EAAE;AACF,oGAAoG;AACpG,iGAAiG;AACjG,iGAAiG;AACjG,6FAA6F;AAC7F,qGAAqG;AACrG,6EAA6E;AAC7E,EAAE;AACF,mGAAmG;AACnG,uFAAuF;AACvF,qGAAqG;AACrG,qFAAqF;AACrF,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AAChE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAczE;;qFAEqF;AACrF,MAAM,UAAU,GAAyD;IACvE,SAAS,EAAE,kBAAkB;IAC7B,YAAY,EAAE,eAAe;IAC7B,MAAM,EAAE,cAAc;CACvB,CAAC;AAEF;;;2EAG2E;AAC3E,SAAS,QAAQ,CAAC,YAAoB;IACpC,OAAO,YAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAC;AACrC,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,UAAU,CAAC,UAAkB,EAAE,MAAc;IAC3D,MAAM,MAAM,GAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC;IAEzE,gGAAgG;IAChG,6FAA6F;IAC7F,MAAM,YAAY,GAAG,IAAI,GAAG,EAAuB,CAAC;IACpD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,CAAC,EAAE,IAAI,EAAE,iBAAiB,EAAE,CAAC,EAAE,CAAC;QAC1D,MAAM,KAAK,GAAG,CAA8B,CAAC;QAC7C,IAAI,OAAO,KAAK,CAAC,YAAY,KAAK,QAAQ;YAAE,SAAS;QACrD,MAAM,IAAI,GAAG,QAAQ,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAC1C,IAAI,GAAG,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACjC,IAAI,CAAC,GAAG,EAAE,CAAC;YAAC,GAAG,GAAG,IAAI,GAAG,EAAE,CAAC;YAAC,YAAY,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;QAAC,CAAC;QAC3D,IAAI,OAAO,KAAK,CAAC,YAAY,KAAK,QAAQ;YAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;IAC1E,CAAC;IAED,KAAK,MAAM,MAAM,IAAI,mBAAmB,EAAE,CAAC;QACzC,MAAM,GAAG,GAAG,IAAI,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;QACrC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC;YAAE,SAAS;QAC/B,KAAK,MAAM,MAAM,IAAI,WAAW,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC;YAC/D,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;gBAAE,SAAS;YACjE,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;YACnD,MAAM,GAAG,GAAG,GAAG,MAAM,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YACvC,IAAI,CAAC;gBACH,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,GAAG,EAAE,MAAM,CAAC,IAAI,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC;gBACtE,MAAM,YAAY,GAAG,SAAS,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC;gBAC/C,sFAAsF;gBACtF,IAAI,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,CAAC,YAAY,CAAC,EAAE,CAAC;oBAC9C,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBACzB,SAAS;gBACX,CAAC;gBACD,cAAc,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,CAAC;gBAC1E,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC1B,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACvF,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/dist/src/version.d.ts

@@ -1,5 +1,5 @@
 /** Engine semver. Keep in lockstep with package.json `version` (enforced by test). */
-export declare const COLTRANE_VERSION = "0.24.13";
+export declare const COLTRANE_VERSION = "0.24.14";
 /**
  * The commit this engine checkout is sitting on, or null when it can't be determined.
  *

package/dist/src/version.js

@@ -17,7 +17,7 @@ import { existsSync, readFileSync, statSync } from "node:fs";
 import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 /** Engine semver. Keep in lockstep with package.json `version` (enforced by test). */
-export const COLTRANE_VERSION = "0.24.13";
+export const COLTRANE_VERSION = "0.24.14";
 /**
  * The commit this engine checkout is sitting on, or null when it can't be determined.
  *

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eir-labs/coltrane",
-  "version": "0.24.13",
+  "version": "0.24.14",
   "description": "A methodology engine \u2014 a typed substrate for defining agents, composing multi-phase standards, dispatching gigs, and sealing every output to a content-addressed ledger. Ships as an MCP server.",
   "type": "module",
   "license": "Apache-2.0",