@tiangong-ai/cli 0.0.58 → 0.0.60

package/dist/research/orchestration.js

@@ -1,6 +1,7 @@
 import { lstat, readFile } from "node:fs/promises";
 import { isAbsolute, join, resolve } from "node:path";
 import { CliError } from "../errors.js";
+import { projectAuthority, projectWithEffectiveAuthority, readProjectAuthorityIndex, } from "./workspace/project-authority.js";
 import { stringifyJson, write } from "../io.js";
 import { parseStrictArgs, strictBoolean, strictString } from "../strict-args.js";
 import { researchSetupHelp, runResearchSetupCommand } from "./setup-command.js";
@@ -9,13 +10,16 @@ import { inspectResearchContext } from "./workspace/context.js";
 import { packageVersion } from "./workspace/constants.js";
 import { researchDataCredentialIds, setCapabilityCredentialValue, } from "./workspace/credentials.js";
 import { configureExternalSkillProfile, doctorExternalCapabilities, EXTERNAL_SKILL_CONTEXT_PROFILE, EXTERNAL_SKILL_MEDIA_PROFILE, EXTERNAL_SKILL_PROFILE, importExternalCapability, inspectExternalSkillCatalog, } from "./workspace/external-skills.js";
-import { appendJournalEvent, readJournal } from "./workspace/journal.js";
+import { appendJournalEvent } from "./workspace/journal.js";
 import { fetchNativeCandidateSource } from "./workspace/broker.js";
 import { preflightEvidenceArtifact, registerEvidenceArtifact } from "./workspace/artifacts.js";
 import { executeResearchDataCapability } from "./workspace/data-evidence-adapter.js";
 import { exportProjectAuditBundle, verifyProjectAuditBundle } from "./workspace/audit-bundle.js";
 import { loadCurrentEvidenceSnapshot } from "./workspace/acquisition.js";
 import { inspectAcquisitionForecast } from "./workspace/acquisition-forecast.js";
+import { reviseProjectAcquisition } from "./workspace/acquisition-revision.js";
+import { approveProjectTaskScope, defineProjectTask, isTaskSchemaName, proposeProjectTaskScope, taskInputSchema, } from "./workspace/task-contract.js";
+import { inspectProjectTask, recordProjectTaskAcceptance, taskAcceptanceInputSchema, } from "./workspace/task-acceptance.js";
 import { freezeEvidenceContentSnapshot, loadCurrentEvidenceContentSnapshot, recordArtifactDecomposition, registerEvidenceAtom, registerEvidenceContentBatch, } from "./workspace/content-evidence.js";
 import { inspectDiscoveryProgress } from "./workspace/discovery-status.js";
 import { EVIDENCE_CONTENT_LIMITS, EVIDENCE_CONTENT_SCHEMA_NAMES, evidenceContentInputSchema, isEvidenceContentSchemaName, } from "./workspace/evidence-content-schema.js";
@@ -104,6 +108,11 @@ export function researchOrchestrationHelp() {
   tiangong-ai research project preflight --question <question> [--goal evidence-report|top-journal] [--policy-project <project-id> --design <absolute-json>] [--requirements <absolute-json>] [--input-plan <absolute-json>] [--workspace <path>] [--json]
   tiangong-ai research project input add <project-id> --path <absolute-file> [--role primary|reference|replication] [--trust-status verified-owner-input|unverified-owner-input|reference-only|replication-candidate] [--independently-reproduced] [--workspace <path>] [--json]
   tiangong-ai research project retry <project-id> [--package <package-id>] [--workspace <path>] [--json]
+  tiangong-ai research project task define <project-id> --input <absolute-json> [--workspace <path>] [--json]
+  tiangong-ai research project task status <project-id> [--workspace <path>] [--json]
+  tiangong-ai research project task acceptance record <project-id> --input <absolute-json> [--workspace <path>] [--json]
+  tiangong-ai research project task scope propose <project-id> --input <absolute-json> --expected-contract <sha256> [--workspace <path>] [--json]
+  tiangong-ai research project task scope approve <project-id> --proposal <sha256> --confirm-change <sha256> [--workspace <path>] [--json]
   tiangong-ai research project fork <source-project-id> --to <target-project-id> [--resume-through discover|acquire|analyze|synthesize] [--design <absolute-json> --design-producer-agent codex|claude --design-producer-session <opaque-id>] [--workspace <path>] [--json]
   tiangong-ai research project addendum <closed-project-id> --to <target-project-id> [--design <absolute-json> --design-producer-agent codex|claude --design-producer-session <opaque-id>] [--workspace <path>] [--json]
   tiangong-ai research project archive <project-id> --reason <text> [--workspace <path>] [--json]
@@ -134,8 +143,9 @@ export function researchOrchestrationHelp() {
   tiangong-ai research project evidence atom register <project-id> --record <absolute-json> [--workspace <path>] [--json]
   tiangong-ai research project evidence content freeze <project-id> [--workspace <path>] [--json]
   tiangong-ai research project evidence content forecast <project-id> --input <absolute-acquisition-audit.json> [--workspace <path>] [--json]
+  tiangong-ai research project evidence acquisition revise <project-id> --expected-snapshot <sha256> --reason <text> [--include-discovery] [--workspace <path>] [--json]
   tiangong-ai research project evidence content status <project-id> [--workspace <path>] [--json]
-  tiangong-ai research schema show <discover|acquire|analyze|synthesize|review|doctor|scientific-design|scientific-assessment-research-design|scientific-assessment-evidence-construct|scientific-assessment-pilot-methods|scientific-review-research-design|scientific-review-evidence-construct|scientific-review-pilot-methods|publication-assessment|publication-review-evidence|publication-review-methods-reproducibility|publication-review-domain-novelty|publication-review-journal-editor> [--compatibility claude-code] [--json]
+  tiangong-ai research schema show <discover|acquire|analyze|synthesize|review|doctor|task-contract|task-scope-change|task-acceptance|scientific-design|scientific-assessment-research-design|scientific-assessment-evidence-construct|scientific-assessment-pilot-methods|scientific-review-research-design|scientific-review-evidence-construct|scientific-review-pilot-methods|publication-assessment|publication-review-evidence|publication-review-methods-reproducibility|publication-review-domain-novelty|publication-review-journal-editor> [--compatibility claude-code] [--json]
   tiangong-ai research status [--project <project-id>] [--all] [--workspace <absolute-path>] [--json]
   tiangong-ai research run [--project <project-id>] [--max-parallel <1-8>] [--max-cycles <1-100>] [--dry-run] [--progress-jsonl] [--workspace <absolute-path>] [--json]
 
@@ -506,7 +516,13 @@ async function runSchema(argv, io) {
         return writeHelp(io);
     const stage = onePositional(args.positionals, "research schema show");
     let schema;
-    if (isEvidenceContentSchemaName(stage)) {
+    if (stage === "task-acceptance") {
+        schema = taskAcceptanceInputSchema();
+    }
+    else if (isTaskSchemaName(stage)) {
+        schema = taskInputSchema(stage);
+    }
+    else if (isEvidenceContentSchemaName(stage)) {
         schema = evidenceContentInputSchema(stage);
     }
     else if (stage === "scientific-design") {
@@ -1025,8 +1041,79 @@ async function runProject(argv, io) {
         }
         throw unknownAction("research project stage", stageAction ?? "");
     }
+    if (action === "task") {
+        const [taskAction, ...taskRest] = rest;
+        if (taskAction === "acceptance") {
+            const [acceptanceAction, ...acceptanceRest] = taskRest;
+            if (acceptanceAction !== "record")
+                throw unknownAction("research project task acceptance", acceptanceAction ?? "");
+            const args = parseStrictArgs(acceptanceRest, { ...WORKSPACE_OPTIONS, input: "string" }, "research project task acceptance record");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project task acceptance record");
+            const result = await recordProjectTaskAcceptance(await workspaceFromArgs(args), projectId, await readBoundedJsonRecord(strictString(args, "input") ?? "", "--input", "RESEARCH_TASK_ACCEPTANCE_INVALID"));
+            writeJson(io, result, args);
+            return 0;
+        }
+        if (taskAction === "scope") {
+            const [scopeAction, ...scopeRest] = taskRest;
+            if (!["propose", "approve"].includes(scopeAction ?? ""))
+                throw unknownAction("research project task scope", scopeAction ?? "");
+            const args = parseStrictArgs(scopeRest, {
+                ...WORKSPACE_OPTIONS,
+                input: "string",
+                "expected-contract": "string",
+                proposal: "string",
+                "confirm-change": "string",
+            }, `research project task scope ${scopeAction}`);
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, `research project task scope ${scopeAction}`);
+            const root = await workspaceFromArgs(args);
+            const result = scopeAction === "approve"
+                ? await approveProjectTaskScope(root, projectId, strictString(args, "proposal") ?? "", strictString(args, "confirm-change"))
+                : await proposeProjectTaskScope(root, projectId, strictString(args, "expected-contract") ?? "", await readBoundedJsonRecord(strictString(args, "input") ?? "", "--input", "RESEARCH_TASK_INVALID"));
+            writeJson(io, result, args);
+            return 0;
+        }
+        if (taskAction !== "define" && taskAction !== "status")
+            throw unknownAction("research project task", taskAction ?? "");
+        const args = parseStrictArgs(taskRest, { ...WORKSPACE_OPTIONS, input: "string" }, `research project task ${taskAction}`);
+        if (strictBoolean(args, "help"))
+            return writeHelp(io);
+        const projectId = onePositional(args.positionals, `research project task ${taskAction}`);
+        const root = await workspaceFromArgs(args);
+        const result = taskAction === "status"
+            ? await inspectProjectTask(root, projectId)
+            : await defineProjectTask(root, projectId, await readBoundedJsonRecord(strictString(args, "input") ?? "", "--input", "RESEARCH_TASK_INVALID"));
+        writeJson(io, result, args);
+        return 0;
+    }
     if (action === "evidence") {
         const [evidenceAction, ...evidenceRest] = rest;
+        if (evidenceAction === "acquisition") {
+            const [revisionAction, ...revisionRest] = evidenceRest;
+            if (revisionAction !== "revise")
+                throw unknownAction("research project evidence acquisition", revisionAction ?? "");
+            const args = parseStrictArgs(revisionRest, {
+                ...WORKSPACE_OPTIONS,
+                "expected-snapshot": "string",
+                reason: "string",
+                "include-discovery": "boolean",
+            }, "research project evidence acquisition revise");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project evidence acquisition revise");
+            const result = await reviseProjectAcquisition({
+                root: await workspaceFromArgs(args),
+                projectId,
+                expectedSnapshotSha256: strictString(args, "expected-snapshot") ?? "",
+                reason: strictString(args, "reason") ?? "",
+                includeDiscovery: strictBoolean(args, "include-discovery"),
+            });
+            writeJson(io, result, args);
+            return 0;
+        }
         if (evidenceAction === "data") {
             const [dataAction, ...dataRest] = evidenceRest;
             if (dataAction !== "run") {
@@ -1287,7 +1374,9 @@ async function runProject(argv, io) {
                 const value = await readBoundedJsonRecord(inputPath, "--input", "RESEARCH_ACQUISITION_FORECAST_INVALID");
                 const result = await inspectAcquisitionForecast(root, projectId, value);
                 writeJson(io, result, args);
-                return result.acquisitionGate.decision === "pass" && !result.knownRoleDeficits.length
+                return result.submissionGate.decision !== "stop" &&
+                    result.acquisitionGate.decision === "pass" &&
+                    !result.knownRoleDeficits.length
                     ? 0
                     : 3;
             }
@@ -1603,12 +1692,8 @@ async function runStatus(argv, io) {
     const root = await workspaceFromArgs(args);
     const config = await loadWorkspaceConfig(root);
     const selectedProject = strictString(args, "project");
-    const workspaceProjects = await listProjects(root);
-    const committedForkTargets = new Set((await readJournal(workspacePaths(root).journal))
-        .filter((event) => event.type === "project.forked" &&
-        isObject(event.payload) &&
-        typeof event.payload.targetProjectId === "string")
-        .map((event) => String(event.payload.targetProjectId)));
+    const authorityIndex = await readProjectAuthorityIndex(root);
+    const workspaceProjects = await listProjects(root, authorityIndex);
     const allProjects = selectedProject
         ? [
             workspaceProjects.find((project) => project.id === selectedProject) ??
@@ -1617,9 +1702,7 @@ async function runStatus(argv, io) {
         : workspaceProjects;
     const projects = selectedProject || strictBoolean(args, "all")
         ? allProjects
-        : allProjects.filter((project) => project.lineage.supersededBy === null &&
-            project.status !== "archived" &&
-            project.status !== "abandoned");
+        : allProjects.filter((project) => ["authoritative", "invalid"].includes(projectAuthority(project, authorityIndex).state));
     const result = {
         workspace: root,
         execution: {
@@ -1638,7 +1721,7 @@ async function runStatus(argv, io) {
         },
         hiddenSupersededProjects: selectedProject || strictBoolean(args, "all")
             ? 0
-            : workspaceProjects.filter((project) => project.lineage.supersededBy !== null).length,
+            : workspaceProjects.filter((project) => authorityIndex.successors.has(project.id)).length,
         hiddenArchivedProjects: selectedProject || strictBoolean(args, "all")
             ? 0
             : workspaceProjects.filter((project) => project.status === "archived").length,
@@ -1646,13 +1729,13 @@ async function runStatus(argv, io) {
             ? 0
             : workspaceProjects.filter((project) => project.status === "abandoned").length,
         projects: await Promise.all(projects.map(async (project) => {
-            const current = refreshProject(project);
-            const authority = projectAuthority(current, workspaceProjects, committedForkTargets);
+            const current = refreshProject(projectWithEffectiveAuthority(project, authorityIndex));
+            const authority = projectAuthority(current, authorityIndex);
             const nativeStage = await inspectNativeResearchStage(root, current);
             const evidencePipeline = await inspectEvidencePipelineForStatus(root, current);
             const snapshot = evidencePipeline.acquisition;
             const readyPackage = nextReadyPackage(current)?.id ?? null;
-            const scientificReview = await inspectScientificReviewStatus(root, current.id);
+            const scientificReview = await inspectScientificReviewStatus(root, current.id, current);
             const evidenceAccess = current.scientificDesign
                 ? await inspectEvidenceAccessForStatus(root, current.id)
                 : null;
@@ -1671,6 +1754,7 @@ async function runStatus(argv, io) {
                 evidencePipeline,
                 nativeStage,
                 scientificReview,
+                task: await inspectProjectTask(root, current.id, authorityIndex.taskEvents.get(current.id) ?? []),
                 evidenceAccess,
                 publication,
                 readyPackage,
@@ -1786,33 +1870,6 @@ async function inspectEvidenceAccessForStatus(root, projectId) {
         };
     }
 }
-function projectAuthority(project, projects, committedForkTargets) {
-    if (project.lineage.kind === "fork" && !committedForkTargets.has(project.id)) {
-        return { state: "invalid", projectId: project.id };
-    }
-    const byId = new Map(projects.map((candidate) => [candidate.id, candidate]));
-    const visited = new Set([project.id]);
-    let current = project;
-    while (current.lineage.supersededBy) {
-        if (visited.has(current.lineage.supersededBy))
-            break;
-        visited.add(current.lineage.supersededBy);
-        const next = byId.get(current.lineage.supersededBy);
-        if (!next)
-            return { state: "superseded", projectId: current.lineage.supersededBy };
-        if (next.lineage.kind === "fork" && !committedForkTargets.has(next.id))
-            break;
-        current = next;
-    }
-    if (project.status === "archived")
-        return { state: "archived", projectId: current.id };
-    if (project.status === "abandoned")
-        return { state: "abandoned", projectId: current.id };
-    return {
-        state: project.id === current.id ? "authoritative" : "superseded",
-        projectId: current.id,
-    };
-}
 async function inspectSnapshotForStatus(root, projectId) {
     const currentPath = join(workspacePaths(root).projects, projectId, "outputs", "evidence-snapshot.json");
     if (!(await pathExists(currentPath)))