@eir-labs/coltrane 0.24.13 → 0.24.15

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 @@
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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 = "0.24.15";
 /**
  * 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 = "0.24.15";
 /**
  * The commit this engine checkout is sitting on, or null when it can't be determined.
  *

package/domain_types/alignment-plan.json

@@ -8,9 +8,15 @@
   "schema": {
     "type": "object",
     "properties": {
-      "gap_summary": { "type": "string" },
-      "alignment_recommendation": { "type": "string" }
+      "gap_summary": {
+        "type": "string"
+      },
+      "alignment_recommendation": {
+        "type": "string"
+      }
     }
   },
-  "required_fields": ["gap_summary"]
+  "required_fields": [
+    "gap_summary"
+  ]
 }

package/domain_types/branch-state.json

@@ -8,9 +8,18 @@
   "schema": {
     "type": "object",
     "properties": {
-      "branch":     { "type": "string", "description": "The git branch to deploy to the preview target." },
-      "commit_sha": { "type": "string", "description": "The branch HEAD commit, sensed directly — the exact commit the preview will build." },
-      "project_id": { "type": "string", "description": "The Vercel project id the branch belongs to, when known at sense time." }
+      "branch": {
+        "type": "string",
+        "description": "The git branch to deploy to the preview target."
+      },
+      "commit_sha": {
+        "type": "string",
+        "description": "The branch HEAD commit, sensed directly — the exact commit the preview will build."
+      },
+      "project_id": {
+        "type": "string",
+        "description": "The Vercel project id the branch belongs to, when known at sense time."
+      }
     }
   },
   "required_fields": [

package/domain_types/change-decision.json

@@ -8,22 +8,47 @@
   "schema": {
     "type": "object",
     "properties": {
-      "scope":                 { "type": "string", "description": "The observable outcome this change commits to." },
-      "non_goals":             { "type": "array", "items": { "type": "string" }, "description": "What this change is NOT, and the neighbouring shapes it must not collapse into." },
-      "stop_condition":        { "type": "string", "description": "The observation at which the work is finished, stated so that someone else could call it." },
+      "scope": {
+        "type": "string",
+        "description": "The observable outcome this change commits to."
+      },
+      "non_goals": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "What this change is NOT, and the neighbouring shapes it must not collapse into."
+      },
+      "stop_condition": {
+        "type": "string",
+        "description": "The observation at which the work is finished, stated so that someone else could call it."
+      },
       "rejected_alternatives": {
         "type": "array",
         "description": "Directions considered and set aside, each with its reason.",
         "items": {
           "type": "object",
           "properties": {
-            "alternative": { "type": "string" },
-            "reason":      { "type": "string" }
+            "alternative": {
+              "type": "string"
+            },
+            "reason": {
+              "type": "string"
+            }
           },
-          "required": ["alternative", "reason"]
+          "required": [
+            "alternative",
+            "reason"
+          ]
         }
       },
-      "risks":                 { "type": "array", "items": { "type": "string" }, "description": "Consequences the direction accepts knowingly." }
+      "risks": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Consequences the direction accepts knowingly."
+      }
     }
   },
   "required_fields": [

package/domain_types/change-plan.json

@@ -8,34 +8,63 @@
   "schema": {
     "type": "object",
     "properties": {
-      "test_first":     {
+      "test_first": {
         "type": "array",
         "description": "The checks that land before the change, each with the failure it is expected to show first.",
         "items": {
           "type": "object",
           "properties": {
-            "check":           { "type": "string" },
-            "expected_before": { "type": "string", "description": "What this check reports while the change is absent." }
+            "check": {
+              "type": "string"
+            },
+            "expected_before": {
+              "type": "string",
+              "description": "What this check reports while the change is absent."
+            }
           },
-          "required": ["check", "expected_before"]
+          "required": [
+            "check",
+            "expected_before"
+          ]
         }
       },
-      "files_touched":  { "type": "array", "items": { "type": "string" }, "description": "Paths the plan commits to changing. A path outside this list is a departure to be recorded, not a silent extension." },
-      "tradeoffs":      {
+      "files_touched": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Paths the plan commits to changing. A path outside this list is a departure to be recorded, not a silent extension."
+      },
+      "tradeoffs": {
         "type": "array",
         "description": "Steps where more than one structure would have served, and why this one was taken.",
         "items": {
           "type": "object",
           "properties": {
-            "at":     { "type": "string" },
-            "chosen": { "type": "string" },
-            "over":   { "type": "string" },
-            "why":    { "type": "string" }
+            "at": {
+              "type": "string"
+            },
+            "chosen": {
+              "type": "string"
+            },
+            "over": {
+              "type": "string"
+            },
+            "why": {
+              "type": "string"
+            }
           },
-          "required": ["at", "chosen", "why"]
+          "required": [
+            "at",
+            "chosen",
+            "why"
+          ]
         }
       },
-      "rollback":       { "type": "string", "description": "How the change is undone if the verdict fails." }
+      "rollback": {
+        "type": "string",
+        "description": "How the change is undone if the verdict fails."
+      }
     }
   },
   "required_fields": [

package/domain_types/change-request.json

@@ -8,13 +8,43 @@
   "schema": {
     "type": "object",
     "properties": {
-      "request_text":        { "type": "string", "description": "The change as stated by the requester, unparaphrased." },
-      "repository":          { "type": "string", "description": "Repository or working-tree identifier the change lands in." },
-      "target_paths":        { "type": "array", "items": { "type": "string" }, "description": "Paths the requester believes are in scope. A belief, not a finding — the reading phase may contradict it." },
-      "acceptance_criteria": { "type": "array", "items": { "type": "string" }, "description": "Observations that would show the change was made. Each entry must be checkable by someone who did not write the change." },
-      "out_of_scope":        { "type": "array", "items": { "type": "string" }, "description": "Work the requester explicitly excludes." },
-      "requested_by":        { "type": "string", "description": "The requesting party." },
-      "change_set_branch":   { "type": "string", "description": "The change-set branch (changeset/<originating-gig-uuid>[/<slug>]) the implementation run must work on. CARRIED here, never inferred from the working tree. Optional and additive: a request that omits it is refused as branch-absent-but-expected only where a run needs it." }
+      "request_text": {
+        "type": "string",
+        "description": "The change as stated by the requester, unparaphrased."
+      },
+      "repository": {
+        "type": "string",
+        "description": "Repository or working-tree identifier the change lands in."
+      },
+      "target_paths": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Paths the requester believes are in scope. A belief, not a finding — the reading phase may contradict it."
+      },
+      "acceptance_criteria": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Observations that would show the change was made. Each entry must be checkable by someone who did not write the change."
+      },
+      "out_of_scope": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Work the requester explicitly excludes."
+      },
+      "requested_by": {
+        "type": "string",
+        "description": "The requesting party."
+      },
+      "change_set_branch": {
+        "type": "string",
+        "description": "The change-set branch (changeset/<originating-gig-uuid>[/<slug>]) the implementation run must work on. CARRIED here, never inferred from the working tree. Optional and additive: a request that omits it is refused as branch-absent-but-expected only where a run needs it."
+      }
     }
   },
   "required_fields": [

package/domain_types/change-set.json

@@ -8,31 +8,60 @@
   "schema": {
     "type": "object",
     "properties": {
-      "diffs":       {
+      "diffs": {
         "type": "array",
         "description": "Per-path patch content, in unified-diff form.",
         "items": {
           "type": "object",
           "properties": {
-            "path":  { "type": "string" },
-            "patch": { "type": "string" }
+            "path": {
+              "type": "string"
+            },
+            "patch": {
+              "type": "string"
+            }
           },
-          "required": ["path", "patch"]
+          "required": [
+            "path",
+            "patch"
+          ]
         }
       },
-      "tests_added": { "type": "array", "items": { "type": "string" }, "description": "Checks introduced by this change, named so a verifier can run exactly them." },
-      "rationale":   { "type": "array", "items": { "type": "string" }, "description": "The non-obvious choices this change makes, each with the reason it was made." },
-      "departures":  {
+      "tests_added": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Checks introduced by this change, named so a verifier can run exactly them."
+      },
+      "rationale": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "The non-obvious choices this change makes, each with the reason it was made."
+      },
+      "departures": {
         "type": "array",
         "description": "Where the artefact left the plan, and why.",
         "items": {
           "type": "object",
           "properties": {
-            "from_step": { "type": "string" },
-            "instead":   { "type": "string" },
-            "why":       { "type": "string" }
+            "from_step": {
+              "type": "string"
+            },
+            "instead": {
+              "type": "string"
+            },
+            "why": {
+              "type": "string"
+            }
           },
-          "required": ["from_step", "instead", "why"]
+          "required": [
+            "from_step",
+            "instead",
+            "why"
+          ]
         }
       }
     }

package/domain_types/change-verdict.json

@@ -8,12 +8,48 @@
   "schema": {
     "type": "object",
     "properties": {
-      "decision_ref":    { "type": "string", "description": "The change-decision this verdict measures against." },
-      "criteria_unmet":  { "type": "array", "items": { "type": "string" }, "description": "Acceptance criteria the change does not meet, stated plainly." },
-      "inferred_not_run": { "type": "array", "items": { "type": "string" }, "description": "Checks that could NOT be executed under the granted tools and were reasoned about instead. Required — an empty list is a claim that everything ran." },
-      "failures_verbatim": { "type": "array", "items": { "type": "string" }, "description": "Failure output as the tool reported it: messages, counts, names. Not summaries of them." },
-      "scope_drift":     { "type": "array", "items": { "type": "string" }, "description": "Where the change exceeded or fell short of the fixed scope." },
-      "recommendation":  { "type": "string", "enum": ["accept", "amend", "reject", "insufficient-evidence"], "description": "insufficient-evidence is the honest answer when the granted tools could not check what the verdict turns on." }
+      "decision_ref": {
+        "type": "string",
+        "description": "The change-decision this verdict measures against."
+      },
+      "criteria_unmet": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Acceptance criteria the change does not meet, stated plainly."
+      },
+      "inferred_not_run": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Checks that could NOT be executed under the granted tools and were reasoned about instead. Required — an empty list is a claim that everything ran."
+      },
+      "failures_verbatim": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Failure output as the tool reported it: messages, counts, names. Not summaries of them."
+      },
+      "scope_drift": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Where the change exceeded or fell short of the fixed scope."
+      },
+      "recommendation": {
+        "type": "string",
+        "enum": [
+          "accept",
+          "amend",
+          "reject",
+          "insufficient-evidence"
+        ],
+        "description": "insufficient-evidence is the honest answer when the granted tools could not check what the verdict turns on."
+      }
     }
   },
   "required_fields": [

package/domain_types/deploy-verdict.json

@@ -8,9 +8,27 @@
   "schema": {
     "type": "object",
     "properties": {
-      "terminal_state":   { "type": "string", "enum": ["READY", "ERROR", "CANCELED", "UNSETTLED"], "description": "The build's terminal readyState, or UNSETTLED when the poll budget was spent before any terminal state was observed." },
-      "logs_tail":        { "type": "array", "items": { "type": "string" }, "description": "The tail of the build log, present only when terminal_state is not READY." },
-      "deadline_exceeded": { "type": "boolean", "description": "True when the bounded poll loop reached its max_tool_calls ceiling without a terminal readyState. Pairs with terminal_state UNSETTLED and pass false." }
+      "terminal_state": {
+        "type": "string",
+        "enum": [
+          "READY",
+          "ERROR",
+          "CANCELED",
+          "UNSETTLED"
+        ],
+        "description": "The build's terminal readyState, or UNSETTLED when the poll budget was spent before any terminal state was observed."
+      },
+      "logs_tail": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "The tail of the build log, present only when terminal_state is not READY."
+      },
+      "deadline_exceeded": {
+        "type": "boolean",
+        "description": "True when the bounded poll loop reached its max_tool_calls ceiling without a terminal readyState. Pairs with terminal_state UNSETTLED and pass false."
+      }
     }
   },
   "required_fields": [

package/domain_types/design-brief.json

@@ -8,23 +8,62 @@
   "schema": {
     "type": "object",
     "properties": {
-      "observations":        {
+      "observations": {
         "type": "array",
         "description": "What was found, each with the locator it was found through.",
         "items": {
           "type": "object",
           "properties": {
-            "observation": { "type": "string" },
-            "locator":     { "type": "string", "description": "Tool plus path or query that produced this observation." }
+            "observation": {
+              "type": "string"
+            },
+            "locator": {
+              "type": "string",
+              "description": "Tool plus path or query that produced this observation."
+            }
           },
-          "required": ["observation"]
+          "required": [
+            "observation"
+          ]
         }
       },
-      "audience_segments":   { "type": "array", "items": { "type": "string" }, "description": "Distinguishable groups the question lands differently for." },
-      "unmet_needs":         { "type": "array", "items": { "type": "string" }, "description": "Needs the current state does not serve. Findings, not proposals." },
-      "adjacent_questions":  { "type": "array", "items": { "type": "string" }, "description": "Questions the exploration surfaced that the posed question did not contain." },
-      "divergence_breadth":  { "type": "string", "enum": ["narrow", "moderate", "wide"], "description": "How far the exploration actually reached, judged against the material available rather than against effort spent." },
-      "unknowns":            { "type": "array", "items": { "type": "string" }, "description": "What the exploration could not determine. Required: the honest bound of the divergence." }
+      "audience_segments": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Distinguishable groups the question lands differently for."
+      },
+      "unmet_needs": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Needs the current state does not serve. Findings, not proposals."
+      },
+      "adjacent_questions": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Questions the exploration surfaced that the posed question did not contain."
+      },
+      "divergence_breadth": {
+        "type": "string",
+        "enum": [
+          "narrow",
+          "moderate",
+          "wide"
+        ],
+        "description": "How far the exploration actually reached, judged against the material available rather than against effort spent."
+      },
+      "unknowns": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "What the exploration could not determine. Required: the honest bound of the divergence."
+      }
     }
   },
   "required_fields": [

package/domain_types/design-concept.json

@@ -8,23 +8,54 @@
   "schema": {
     "type": "object",
     "properties": {
-      "concept_name":    { "type": "string", "description": "Short handle for the concept." },
-      "description":     { "type": "string", "description": "What it is, in the audience's register." },
-      "mechanism":       { "type": "array", "items": { "type": "string" }, "description": "How it works, step by step. The part that distinguishes a concept from a wish." },
-      "addresses":       { "type": "array", "items": { "type": "string" }, "description": "Which success criteria from the definition this concept answers, named individually." },
-      "tradeoffs":       {
+      "concept_name": {
+        "type": "string",
+        "description": "Short handle for the concept."
+      },
+      "description": {
+        "type": "string",
+        "description": "What it is, in the audience's register."
+      },
+      "mechanism": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "How it works, step by step. The part that distinguishes a concept from a wish."
+      },
+      "addresses": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "Which success criteria from the definition this concept answers, named individually."
+      },
+      "tradeoffs": {
         "type": "array",
         "description": "What this concept gives up, and what it buys with it.",
         "items": {
           "type": "object",
           "properties": {
-            "gives_up": { "type": "string" },
-            "buys":     { "type": "string" }
+            "gives_up": {
+              "type": "string"
+            },
+            "buys": {
+              "type": "string"
+            }
           },
-          "required": ["gives_up", "buys"]
+          "required": [
+            "gives_up",
+            "buys"
+          ]
         }
       },
-      "open_questions":  { "type": "array", "items": { "type": "string" }, "description": "What remains unresolved in the concept as built." }
+      "open_questions": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        },
+        "description": "What remains unresolved in the concept as built."
+      }
     }
   },
   "required_fields": [