kibi-cli 2.4.0 → 2.5.1

package/dist/operations/planning/apply-plan.js

@@ -9,15 +9,20 @@ import { executeStatus } from "../../public/operations/discovery-executors.js";
 import { PREDICATE_SCHEMA_ALIGNMENT_CODE, migrationPlanHash, } from "../../public/operations/migration-plan.js";
 import { readMigrationConfigStatus } from "../../public/operations/migration-plan.js";
 import { readWorkspaceSnapshot } from "../../public/operations/workspace-snapshot.js";
+import { computeShardPath, renderShardWithRelationship, } from "../../relationships/shards.js";
 import { canonicalFilesystemPath } from "../../utils/canonical-path.js";
 import { isDerivedKbPath } from "../../utils/kb-paths.js";
 import { bootstrapEmptyKbSnapshotId, bootstrapPlanHash, } from "../bootstrap/types.js";
+import { validateBootstrapPayload } from "../bootstrap/validation.js";
+import { SCHEMA6_AUTOMATIC_CODES, applySchema6MigrationAction, } from "../migration/schema6.js";
+import { buildUpsertBatchCommitGoal, formatUpsertError, } from "../mutation/contradictions.js";
 import { executeDelete } from "../mutation/delete.js";
-import { retirePendingSourceReceipt, writePendingSourceReceipt, } from "../mutation/source-authoring.js";
-import { executeUpsert } from "../mutation/upsert.js";
+import { PLAN_APPLY_JOURNAL_VERSION, contentHash, createPlanApplyJournal, isPlanApplyJournalId, openPlanApplyJournal, openPlanApplyJournalById, planRecoveryNotes, publishJournaledFiles, reconcilePendingSourceReceipts, recordPlanApplyJournal, recoverPlanApplyJournal, restoreJournaledFiles, settlePendingPlanApplyJournals, storeFingerprint, withPlanRecoveryNotes, } from "../mutation/plan-apply-journal.js";
+import { canonicalSourcePath, renderSourceDocument, } from "../mutation/source-authoring.js";
+import { assertRelationshipShardContained, executeUpsert, validateUpsertForCommit, } from "../mutation/upsert.js";
 import { acquireWorkspaceMutationLock, releaseWorkspaceMutationLock, } from "../mutation/workspace-mutation-lock.js";
-import { compilePlanHash, } from "./compile-intent.js";
-// implements REQ-kibi-change-to-proof-plan-compiler
+import { compilePlanHash, isBlockingWitness, parseWhatIfAnalysis, planWhatIfGoal, } from "./compile-intent.js";
+// implements REQ-kibi-change-to-proof-plan-compiler-v2
 export const PLAN_APPLY_RESULT_VERSION = "kibi.plan-apply-result.v1";
 const ENTITY_TYPES = new Set([
     "req",
@@ -38,21 +43,6 @@ function isRecord(value) {
 function digest(value) {
     return createHash("sha256").update(value).digest("hex");
 }
-/**
- * Reconcile pending-source receipts with committed source writes: a written
- * file is bound to its exact bytes until Git tracks it, and a deleted file
- * must not leave a receipt that later syncs would report as missing.
- */
-function reconcilePendingSourceReceipts(workspaceRoot, writes) {
-    for (const write of writes) {
-        if ((write.mode ?? "write") === "delete") {
-            retirePendingSourceReceipt(workspaceRoot, write.path);
-        }
-        else if (write.afterHash !== null) {
-            writePendingSourceReceipt(workspaceRoot, write.path, write.afterHash);
-        }
-    }
-}
 function relationships(step) {
     if (!Array.isArray(step.relationships))
         return [];
@@ -191,7 +181,8 @@ function validateBootstrapPlanShape(args) {
         throw new Error("Bootstrap apply failed: ready plans require exact branch, KB snapshot, and workspace snapshot bindings");
     }
     if (!/^[a-f0-9]{64}$/i.test(plan.expected.kbSnapshotId) &&
-        !/^empty-source-state-[a-f0-9]{64}$/i.test(plan.expected.kbSnapshotId)) {
+        !/^empty-source-state-[a-f0-9]{64}$/i.test(plan.expected.kbSnapshotId) &&
+        !/^generation-[^:\s]+:\d+$/.test(plan.expected.kbSnapshotId)) {
         throw new Error("Bootstrap apply failed: ready plans require an exact KB snapshot binding");
     }
     for (const [sourcePath, sourceHash] of Object.entries(plan.expected.sourceHashes)) {
@@ -204,6 +195,33 @@ function validateBootstrapPlanShape(args) {
         throw new Error("Bootstrap apply failed: ready plans must contain actions");
     return orderBootstrapActions(plan.actions);
 }
+// implements REQ-KIBI-BOOTSTRAP-PLAN
+function preflightBootstrapActions(actions, context) {
+    for (const action of actions) {
+        try {
+            const input = validateBootstrapPayload(action.payload, context.clock());
+            if (input.document?.path !== undefined)
+                canonicalSourcePath(context, input, {
+                    id: input.id,
+                    ...input.properties,
+                });
+        }
+        catch (error) {
+            throw new OperationError("BOOTSTRAP_PLAN_INVALID", `Bootstrap action ${action.id} is invalid: ${error instanceof Error ? error.message : String(error)}. Re-plan before applying; no bootstrap writes or journal were created.`, false);
+        }
+    }
+}
+// implements REQ-KIBI-BOOTSTRAP-PLAN
+function isDeterministicBootstrapFailure(error) {
+    const detail = error instanceof Error ? error.message : String(error);
+    return (/(?:Entity|Relationship) validation failed|Proposition-complete ingestion failed|Contradiction detected for requirement|(?:'type' and 'id' are required|unsupported step entity type|every step needs an entity id)/i.test(detail) ||
+        (error instanceof OperationError &&
+            [
+                "BOOTSTRAP_PLAN_INVALID",
+                "SOURCE_PATH_INVALID",
+                "DOCUMENT_PATH_REQUIRED",
+            ].includes(error.code)));
+}
 function isEntityDeletionApplyArgs(args) {
     return "plan" in args && args.plan.version === "kibi.entity-deletion-plan.v1";
 }
@@ -307,6 +325,48 @@ async function validateSources(context, sourceHashes) {
     }
     return checked;
 }
+/**
+ * Validate one approved source write against the live workspace: the target
+ * must be workspace-relative, stay inside the workspace (also through
+ * symlinks), avoid Kibi's derived runtime trees, still hold the approved
+ * before-bytes, and carry an after-hash that matches its staged body.
+ */
+async function resolveSourceWriteTarget(workspaceRoot, fsPort, write) {
+    if (!write.path ||
+        path.isAbsolute(write.path) ||
+        write.path.split(/[\\/]/).includes("..")) {
+        throw new Error(`Apply plan failed: sourceWrites.path must be workspace-relative: ${write.path}`);
+    }
+    const absolute = path.resolve(workspaceRoot, write.path);
+    const root = path.resolve(workspaceRoot);
+    assertSourceWriteStaysInWorkspace(root, absolute, write.path);
+    const relative = path.relative(root, absolute).split(path.sep).join("/");
+    if (relative === ".kb" || isDerivedKbPath(relative)) {
+        throw new Error("Apply plan failed: sourceWrites.path cannot target Kibi's derived .kb runtime trees");
+    }
+    const realRoot = canonicalFilesystemPath(root);
+    const realExisting = canonicalFilesystemPath(absolute);
+    if (realExisting !== realRoot &&
+        !realExisting.startsWith(`${realRoot}${path.sep}`)) {
+        throw new Error(`Apply plan failed: sourceWrites.path follows a symlink outside the workspace: ${write.path}`);
+    }
+    const existing = await fsPort.readFile(absolute).catch(() => undefined);
+    const beforeHash = existing === undefined ? null : digest(existing);
+    if (beforeHash !== write.beforeHash) {
+        throw new Error(`Apply plan failed: source hash changed for ${write.path}`);
+    }
+    const mode = write.mode ?? "write";
+    if (mode === "write" &&
+        (write.body === undefined ||
+            write.afterHash === null ||
+            digest(write.body) !== write.afterHash)) {
+        throw new Error(`Apply plan failed: afterHash does not match staged body for ${write.path}`);
+    }
+    if (mode === "delete" && write.afterHash !== null) {
+        throw new Error(`Apply plan failed: delete source write must have a null afterHash for ${write.path}`);
+    }
+    return { absolute, relative, existing, mode };
+}
 async function applySourceWrites(context, writes, planHash, allowReplay = false, onCommitted = () => undefined) {
     if (writes.length === 0) {
         return { paths: [], rollback: async () => undefined, journalId: null };
@@ -412,44 +472,7 @@ async function applySourceWrites(context, writes, planHash, allowReplay = false,
     try {
         // Validate every target and hash before touching the working tree.
         for (const write of writes) {
-            if (!write.path ||
-                path.isAbsolute(write.path) ||
-                write.path.split(/[\\/]/).includes("..")) {
-                throw new Error(`Apply plan failed: sourceWrites.path must be workspace-relative: ${write.path}`);
-            }
-            const absolute = path.resolve(context.workspaceRoot, write.path);
-            const root = path.resolve(context.workspaceRoot);
-            assertSourceWriteStaysInWorkspace(root, absolute, write.path);
-            const workspaceRelative = path
-                .relative(root, absolute)
-                .split(path.sep)
-                .join("/");
-            if (workspaceRelative === ".kb" || isDerivedKbPath(workspaceRelative)) {
-                throw new Error("Apply plan failed: sourceWrites.path cannot target Kibi's derived .kb runtime trees");
-            }
-            const realRoot = canonicalFilesystemPath(root);
-            const realExisting = canonicalFilesystemPath(absolute);
-            if (realExisting !== realRoot &&
-                !realExisting.startsWith(`${realRoot}${path.sep}`)) {
-                throw new Error(`Apply plan failed: sourceWrites.path follows a symlink outside the workspace: ${write.path}`);
-            }
-            const existing = await context.fs
-                .readFile(absolute)
-                .catch(() => undefined);
-            const beforeHash = existing === undefined ? null : digest(existing);
-            if (beforeHash !== write.beforeHash) {
-                throw new Error(`Apply plan failed: source hash changed for ${write.path}`);
-            }
-            const mode = write.mode ?? "write";
-            if (mode === "write" &&
-                (write.body === undefined ||
-                    write.afterHash === null ||
-                    digest(write.body) !== write.afterHash)) {
-                throw new Error(`Apply plan failed: afterHash does not match staged body for ${write.path}`);
-            }
-            if (mode === "delete" && write.afterHash !== null) {
-                throw new Error(`Apply plan failed: delete source write must have a null afterHash for ${write.path}`);
-            }
+            const { absolute, existing, mode } = await resolveSourceWriteTarget(context.workspaceRoot, fsPort, write);
             originals.push({ absolute, body: existing });
             paths.push(write.path);
             const stageBase = path.join(context.workspaceRoot, ".kb", "recovery", `${journalId}-${entries.length}`);
@@ -656,6 +679,7 @@ async function executeBootstrapPlan(args, context, recovery = false, remainingAc
     const actions = recovery
         ? [...(remainingActions ?? args.plan.actions)]
         : validateBootstrapPlanShape(args);
+    preflightBootstrapActions(actions, context);
     const prolog = context.prolog ?? (await context.ensureProlog?.());
     if (!prolog)
         throw new Error("Bootstrap apply requires a Prolog runtime");
@@ -828,19 +852,22 @@ async function executeBootstrapPlan(args, context, recovery = false, remainingAc
             }
             catch (error) {
                 const detail = error instanceof Error ? error.message : String(error);
+                const deterministic = isDeterministicBootstrapFailure(error);
                 results.push({ actionId: action.id, outcome: "failed", detail });
-                failures.push({ actionId: action.id, detail });
-                await writeJournal("repair_required", activeActionId, lastCheckpoint);
+                failures.push({ actionId: action.id, detail, deterministic });
+                await writeJournal(deterministic ? "rejected" : "repair_required", activeActionId, lastCheckpoint);
                 return {
                     content: [
                         {
                             type: "text",
-                            text: `Bootstrap plan ${args.plan.planHash.slice(0, 12)} partially applied; repair journal ${journalId}.`,
+                            text: deterministic
+                                ? `Bootstrap plan rejected at ${action.id}: ${detail}. ${results.filter((row) => row.outcome === "applied").length} action(s) committed; re-plan from the current state.`
+                                : `Bootstrap plan ${args.plan.planHash.slice(0, 12)} partially applied; repair journal ${journalId}.`,
                         },
                     ],
                     structuredContent: {
                         version: PLAN_APPLY_RESULT_VERSION,
-                        outcome: "partially_applied",
+                        outcome: deterministic ? "rejected" : "partially_applied",
                         planHash: args.plan.planHash,
                         actionResults: results,
                         changedEntities,
@@ -859,16 +886,24 @@ async function executeBootstrapPlan(args, context, recovery = false, remainingAc
                             sourceHashesChecked: Object.keys(args.plan.expected.sourceHashes)
                                 .length,
                             notes: [
-                                "Bootstrap application stopped at a repairable action failure.",
+                                deterministic
+                                    ? "Bootstrap stopped at a deterministic action failure; the journal is terminal. Re-plan from the current state."
+                                    : "Bootstrap application stopped at a repairable action failure.",
                             ],
                         },
-                        status: "committed_with_repairs",
+                        status: deterministic ? "rejected" : "committed_with_repairs",
                         effectFailures: failures,
                         nextActions: [
                             {
-                                operation: "kb_apply_plan",
-                                input: { recoveryJournalId: journalId },
-                                reason: "Resume the remaining bootstrap actions from the immutable recovery journal; do not retry the original plan.",
+                                operation: deterministic
+                                    ? "kb_plan_bootstrap"
+                                    : "kb_apply_plan",
+                                ...(deterministic
+                                    ? {}
+                                    : { input: { recoveryJournalId: journalId } }),
+                                reason: deterministic
+                                    ? "Re-plan a corrected bootstrap from the current state; this journal cannot be replayed."
+                                    : "Resume the remaining bootstrap actions from the immutable recovery journal; do not retry the original plan.",
                                 required: true,
                             },
                         ],
@@ -963,9 +998,29 @@ async function executeBootstrapPlan(args, context, recovery = false, remainingAc
         },
     };
 }
-// implements REQ-kibi-change-to-proof-plan-compiler, REQ-agent-guided-migration-orchestration
+// implements REQ-kibi-change-to-proof-plan-compiler-v2, REQ-core-atomic-upsert-persistence
 async function executeApplyPlanUnlocked(args, context, onCommitted = () => undefined) {
+    // Finish any interrupted plan application before this call reads or writes
+    // anything, and report what was done alongside this call's own result.
+    const recovered = await recoverInterruptedPlans(context, "recoveryJournalId" in args ? args.recoveryJournalId : undefined);
+    if (recovered.some((recovery) => recovery.action !== "none"))
+        onCommitted();
+    let result;
+    try {
+        result = await dispatchApplyPlan(args, context, onCommitted, recovered);
+    }
+    catch (error) {
+        // A plan compiled before the recovery commonly fails its snapshot check
+        // now; the failure still names the interrupted plan that was settled.
+        throw withPlanRecoveryNotes(error, planRecoveryNotes(recovered));
+    }
+    return withRecoveryReport(result, recovered);
+}
+// implements REQ-kibi-change-to-proof-plan-compiler-v2, REQ-agent-guided-migration-orchestration
+async function dispatchApplyPlan(args, context, onCommitted, recovered) {
     if ("recoveryJournalId" in args) {
+        if (isPlanApplyJournalId(args.recoveryJournalId))
+            return executePlanJournalRecovery(args.recoveryJournalId, context, recovered);
         if (args.recoveryJournalId.startsWith("bootstrap-")) {
             if (!context.fs)
                 throw new Error("Bootstrap recovery requires a filesystem-capable runtime");
@@ -977,6 +1032,10 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
                 journal.kind !== "bootstrap" ||
                 !journal.plan)
                 throw new Error("Bootstrap recovery journal is invalid");
+            if (journal.state === "rejected" ||
+                (journal.results ?? []).some((row) => row.outcome === "failed" &&
+                    isDeterministicBootstrapFailure(new Error(String(row.detail)))))
+                throw new OperationError("BOOTSTRAP_PLAN_REJECTED", "Bootstrap recovery refused: deterministic failure is terminal; re-plan from the current state.", false);
             if (!/^[a-f0-9]{64}$/i.test(journal.plan.planHash) ||
                 bootstrapPlanHash(journal.plan) !== journal.plan.planHash)
                 throw new Error("Bootstrap recovery journal plan hash is invalid");
@@ -1098,7 +1157,428 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
             },
         };
     }
+    return executeCompilePlan(args, context, onCommitted, recovered);
+}
+// implements REQ-kibi-truthful-consistency
+/**
+ * Run every step through the validation chain executeUpsert runs. Each step
+ * is validated against the live store plus what the earlier steps will have
+ * written by then (`staged`): entities they create count as relationship
+ * targets, their kinds and claim keys are read from the plan, their
+ * relationships merge into a later upsert of the same entity, and their
+ * predicate schemas govern later predicate facts.
+ */
+async function validatePlanSteps(steps, context) {
+    const stagedEntities = new Map();
+    const stagedRelationships = [];
+    const validated = [];
+    for (const step of steps) {
+        try {
+            const { validated: result } = await validateUpsertForCommit(step, context, {
+                staged: {
+                    entities: stagedEntities,
+                    relationships: [...stagedRelationships],
+                },
+            });
+            stagedEntities.set(step.id, result.entity);
+            stagedRelationships.push(...result.relationships);
+            validated.push({
+                input: step,
+                entity: result.entity,
+                relationships: result.relationships,
+            });
+        }
+        catch (error) {
+            throw new Error(`step ${step.id} is invalid: ${error instanceof Error ? error.message : String(error)}`);
+        }
+    }
+    return validated;
+}
+/**
+ * Every workspace file the plan changes, with exact before/after bytes: the
+ * plan's approved sourceWrites, the authored document of every entity step,
+ * and the relationship shards its steps append, each rendered exactly as
+ * executeUpsert would write it, in step order. `sources` maps a step index to
+ * its document, which becomes the committed entity's `source`.
+ */
+// implements REQ-kibi-change-to-proof-plan-compiler-v2
+async function planFileWrites(context, prolog, fsPort, sourceWrites, steps, now) {
+    const workspaceRoot = context.workspaceRoot;
+    const files = new Map();
+    for (const write of sourceWrites) {
+        const target = await resolveSourceWriteTarget(workspaceRoot, fsPort, write);
+        if (files.has(target.relative)) {
+            throw new Error(`Apply plan failed: sourceWrites lists ${write.path} more than once`);
+        }
+        if (target.mode === "delete" && !fsPort.unlink) {
+            throw new Error(`Apply plan failed: delete requires filesystem unlink support: ${write.path}`);
+        }
+        const before = target.existing ?? null;
+        const after = target.mode === "write" ? (write.body ?? "") : null;
+        files.set(target.relative, {
+            path: target.relative,
+            origin: "plan",
+            mode: target.mode,
+            before,
+            beforeHash: before === null ? null : contentHash(before),
+            after,
+            afterHash: after === null ? null : contentHash(after),
+        });
+    }
+    // Entity documents: the bytes kb_upsert would publish for the validated
+    // entity, merged into the document as the plan leaves it. A plan without
+    // them leaves its entities only in the branch store, so a rebuild or a
+    // fresh clone loses them. Symbols keep the kb_upsert path, which also
+    // refreshes their generated coordinates.
+    const sources = new Map();
+    for (const [index, step] of steps.entries()) {
+        if (step.input.type === "symbol")
+            continue;
+        const [existing] = step.input.document?.path === undefined
+            ? await loadEntities(prolog, {
+                id: step.input.id,
+                type: step.input.type,
+            })
+            : [];
+        const relative = canonicalSourcePath(context, step.input, step.entity, existing);
+        let file = files.get(relative);
+        if (file === undefined) {
+            // canonicalSourcePath already refused traversal, derived .kb trees and
+            // symlinks that leave the workspace.
+            const existingBytes = await fsPort
+                .readFile(path.join(workspaceRoot, relative))
+                .catch(() => undefined);
+            const before = existingBytes ?? null;
+            file = {
+                path: relative,
+                origin: "entity-document",
+                mode: "write",
+                before,
+                beforeHash: before === null ? null : contentHash(before),
+                after: before,
+                afterHash: before === null ? null : contentHash(before),
+            };
+            files.set(relative, file);
+        }
+        if (file.mode === "delete") {
+            throw new Error(`Apply plan failed: step ${step.input.id} writes ${relative}, which the plan deletes`);
+        }
+        sources.set(index, relative);
+        // A plan sourceWrite for the same file is approved, byte-exact content:
+        // it is the document, not a base to render into.
+        if (file.origin === "plan")
+            continue;
+        const after = renderSourceDocument(step.input, step.entity, file.after ?? undefined, relative);
+        file.after = after;
+        file.afterHash = contentHash(after);
+    }
+    const root = path.resolve(workspaceRoot);
+    const kbRoot = path.join(workspaceRoot, ".kb");
+    const createdAt = now.toISOString();
+    for (const step of steps) {
+        for (const relationship of step.relationships) {
+            const type = typeof relationship.type === "string" ? relationship.type : "";
+            const from = typeof relationship.from === "string"
+                ? relationship.from
+                : step.input.id;
+            const to = typeof relationship.to === "string" ? relationship.to : "";
+            if (!type || !from || !to)
+                continue;
+            const shardPath = computeShardPath(kbRoot, from);
+            assertRelationshipShardContained(workspaceRoot, shardPath);
+            const relative = path
+                .relative(root, path.resolve(shardPath))
+                .split(path.sep)
+                .join("/");
+            let file = files.get(relative);
+            if (file === undefined) {
+                const existing = await fsPort.readFile(shardPath).catch(() => null);
+                const existingHash = existing === null ? null : contentHash(existing);
+                file = {
+                    path: relative,
+                    origin: "relationship-shard",
+                    mode: "write",
+                    before: existing,
+                    beforeHash: existingHash,
+                    after: existing,
+                    afterHash: existingHash,
+                };
+                files.set(relative, file);
+            }
+            const next = renderShardWithRelationship(shardPath, file.after, {
+                type,
+                from,
+                to,
+                created_at: createdAt,
+                created_by: "kibi/upsert",
+                source: "mcp://kibi/upsert",
+            });
+            if (next !== null) {
+                file.mode = "write";
+                file.after = next;
+                file.afterHash = contentHash(next);
+            }
+        }
+    }
+    return {
+        files: [...files.values()].filter((file) => file.origin === "plan" ||
+            file.origin === "entity-document" ||
+            file.afterHash !== file.beforeHash),
+        sources,
+    };
+}
+function errorMessage(error) {
+    return error instanceof Error ? error.message : String(error);
+}
+// implements REQ-kibi-change-to-proof-plan-compiler-v2, REQ-core-atomic-upsert-persistence
+/**
+ * Apply a validated compile plan all-or-nothing:
+ * 1. journal every file change (exact bytes) and every store upsert, plus a
+ *    fingerprint of the touched store entities, before the first write;
+ * 2. publish the files with temp-file + rename (fsync where available);
+ * 3. commit every step in one Prolog batch transaction — the only commit
+ *    point.
+ * Any failure before the commit restores every file from the journal and
+ * leaves the store untouched; an interrupted application is completed or
+ * rolled back from the journal by the next mutating call.
+ */
+async function commitCompilePlan(context, prolog, plan, steps, revalidate, now, onCommitted) {
+    // Store upserts, one per step. A step with an authored document commits
+    // that document as its source, exactly as a source-first kb_upsert does.
+    const storeEntries = (sources = new Map()) => steps.map((step, index) => {
+        const source = sources.get(index);
+        return {
+            entity: source === undefined ? step.entity : { ...step.entity, source },
+            relationships: step.relationships,
+            skipContradictionCheck: step.input._skipContradictionCheck === true,
+        };
+    });
+    let entries = storeEntries();
+    const entityIds = [
+        ...new Set(entries.map((entry) => String(entry.entity.id))),
+    ];
+    const changedRelationships = entries.reduce((sum, entry) => sum + entry.relationships.length, 0);
+    const storeRejection = (result) => new Error(`the store rejected the plan's batch transaction: ${formatUpsertError(entityIds.length === 1
+        ? String(entityIds[0])
+        : `plan batch [${entityIds.join(", ")}]`, result.error, result.errorRecord)}`);
+    const fsPort = context.fs;
+    if (fsPort === undefined) {
+        if (plan.sourceWrites.length > 0) {
+            throw new Error("Apply plan failed: sourceWrites require a filesystem-capable runtime");
+        }
+        // Without a filesystem there are no workspace files to coordinate: the
+        // single store transaction is the whole application.
+        const written = await prolog.query(buildUpsertBatchCommitGoal(entries));
+        if (!written.success) {
+            throw new Error(`Apply plan failed; no change was applied: ${storeRejection(written).message}`);
+        }
+        onCommitted();
+        prolog.invalidateCache?.();
+        return {
+            journalId: null,
+            changedEntities: entries.length,
+            changedRelationships,
+            documentPaths: [],
+            effectFailures: [],
+            nextActions: [],
+        };
+    }
+    const slot = openPlanApplyJournal(context, plan.planHash);
+    if (slot.existing?.state === "committed") {
+        throw new OperationError("MUTATION_ALREADY_COMMITTED", `MUTATION_ALREADY_COMMITTED: plan ${plan.planHash} was already applied (journal ${slot.journalId}); compile a fresh plan instead of applying it again`, false);
+    }
+    if (slot.existing !== null && slot.existing.state !== "rolled_back") {
+        throw new OperationError("PLAN_APPLY_RECOVERY_REQUIRED", `Plan ${plan.planHash} has an unfinished journal ${slot.journalId}; run kb_apply_plan with recoveryJournalId=${slot.journalId} before applying it again`, false);
+    }
+    const { files, sources } = await planFileWrites(context, prolog, fsPort, plan.sourceWrites, steps, now);
+    entries = storeEntries(sources);
+    const goal = buildUpsertBatchCommitGoal(entries);
+    const documentPaths = [
+        ...new Set([
+            ...plan.sourceWrites.map((write) => write.path),
+            ...sources.values(),
+        ]),
+    ];
+    let preCommitFingerprint;
+    try {
+        preCommitFingerprint = await storeFingerprint(prolog, entityIds);
+    }
+    catch (error) {
+        throw new Error(`Apply plan failed before any write: the store could not be fingerprinted for the plan journal: ${errorMessage(error)}`);
+    }
+    const handle = createPlanApplyJournal(slot.journalPath, {
+        version: PLAN_APPLY_JOURNAL_VERSION,
+        journalId: slot.journalId,
+        planHash: plan.planHash,
+        branch: slot.branch,
+        state: "prepared",
+        createdAt: now.toISOString(),
+        updatedAt: now.toISOString(),
+        files,
+        store: { entityIds, preCommitFingerprint, entries },
+        summary: {
+            planPaths: plan.sourceWrites.map((write) => write.path),
+            filePaths: files.map((file) => file.path),
+            changedEntities: entries.length,
+            changedRelationships,
+        },
+    });
+    const rollBack = async (error, phase) => {
+        let restored;
+        try {
+            restored = await restoreJournaledFiles(fsPort, context.workspaceRoot, handle.journalPath, files);
+        }
+        catch (rollbackError) {
+            throw new OperationError("PLAN_APPLY_RECOVERY_REQUIRED", `Plan ${plan.planHash} failed ${phase} (${errorMessage(error)}), and restoring its source writes also failed (${errorMessage(rollbackError)}). Journal ${slot.journalId} is kept: the next kb_apply_plan or kb_upsert call rolls it back, or run kb_apply_plan with recoveryJournalId=${slot.journalId}`, false);
+        }
+        const detail = `Plan ${plan.planHash.slice(0, 12)} failed ${phase}; no change was applied: the store is unchanged and ${restored.length} source file(s) were restored from journal ${slot.journalId}.`;
+        try {
+            recordPlanApplyJournal(handle, {
+                state: "rolled_back",
+                resolution: { action: "rolled_back", by: "apply", detail },
+            });
+        }
+        catch {
+            // The files are restored and the store never committed, so a journal
+            // left in an earlier state resolves to the same rollback next time.
+        }
+        const message = `Apply plan failed ${phase}; no change was applied (store unchanged, ${restored.length} source file(s) restored from journal ${slot.journalId}): ${errorMessage(error)}`;
+        if (error instanceof OperationError) {
+            throw new OperationError(error.code, message, error.retryable);
+        }
+        throw new Error(message);
+    };
+    try {
+        await publishJournaledFiles(fsPort, context.workspaceRoot, files);
+    }
+    catch (error) {
+        return rollBack(error, "while publishing its source writes");
+    }
+    if (plan.sourceWrites.length > 0) {
+        // Steps were validated against the workspace as it was; validate them
+        // again against the published source bytes before the commit.
+        try {
+            await revalidate();
+        }
+        catch (error) {
+            return rollBack(error, "validation against its published source writes");
+        }
+    }
+    try {
+        recordPlanApplyJournal(handle, { state: "store_committing" });
+    }
+    catch (error) {
+        return rollBack(error, "while journaling its store commit");
+    }
+    let written;
+    let commitFailure;
+    try {
+        written = await prolog.query(goal);
+        if (!written.success)
+            commitFailure = storeRejection(written);
+    }
+    catch (error) {
+        commitFailure = error;
+    }
+    const effectFailures = [];
+    const nextActions = [];
+    if (commitFailure !== undefined) {
+        // The batch is one transaction: it either changed the plan's entities or
+        // changed nothing. Decide from the store, not from the transport.
+        let fingerprint;
+        try {
+            fingerprint = await storeFingerprint(prolog, entityIds);
+        }
+        catch (probeError) {
+            if (written === undefined) {
+                throw new OperationError("PLAN_APPLY_RECOVERY_REQUIRED", `Plan ${plan.planHash} lost contact with the store during its commit (${errorMessage(commitFailure)}), and the store could not be inspected (${errorMessage(probeError)}). Journal ${slot.journalId} is kept: the next kb_apply_plan or kb_upsert call completes or rolls it back, or run kb_apply_plan with recoveryJournalId=${slot.journalId}`, false);
+            }
+            // The store answered with a rejection; trust it.
+        }
+        if (fingerprint === undefined || fingerprint === preCommitFingerprint) {
+            return rollBack(commitFailure, "at its store commit");
+        }
+        effectFailures.push({
+            kind: "store-commit",
+            errorCode: "STORE_COMMIT_REPORTED_FAILURE",
+            detail: `The store reported a failure (${errorMessage(commitFailure)}) but shows the plan's batch committed; the plan is kept as applied.`,
+        });
+        nextActions.push({
+            operation: "kb_status",
+            reason: "The store committed the plan's batch while reporting a failure; confirm the branch snapshot is persisted before further writes.",
+            required: true,
+        }, {
+            operation: "kb_check",
+            reason: "Run the consistency checks after the unconfirmed store commit and follow their typed repair actions.",
+            required: true,
+        });
+    }
+    // The batch transaction committed: every step is in the store.
+    onCommitted();
+    prolog.invalidateCache?.();
+    try {
+        recordPlanApplyJournal(handle, { state: "store_committed" });
+    }
+    catch {
+        // A journal left at store_committing is completed on the next call: the
+        // store fingerprint now shows the commit.
+    }
+    try {
+        reconcilePendingSourceReceipts(context.workspaceRoot, files);
+    }
+    catch (error) {
+        effectFailures.push({
+            kind: "pending-source-receipt",
+            errorCode: "PENDING_SOURCE_RECEIPT_FAILED",
+            detail: errorMessage(error),
+        });
+        nextActions.push({
+            operation: "kb_apply_plan",
+            input: { recoveryJournalId: slot.journalId },
+            reason: "The plan committed, but binding its new source files to pending-source receipts failed; recovering the journal finishes the receipts. Do not apply the original plan again.",
+            required: true,
+        });
+        return {
+            journalId: slot.journalId,
+            changedEntities: entries.length,
+            changedRelationships,
+            documentPaths,
+            effectFailures,
+            nextActions,
+        };
+    }
+    try {
+        recordPlanApplyJournal(handle, {
+            state: "committed",
+            resolution: {
+                action: "completed",
+                by: "apply",
+                detail: `Applied plan ${plan.planHash.slice(0, 12)}: ${entries.length} step(s) in one store transaction and ${files.length} journaled file(s).`,
+            },
+        });
+    }
+    catch {
+        // A store_committed journal completes idempotently on the next call.
+    }
+    return {
+        journalId: slot.journalId,
+        changedEntities: entries.length,
+        changedRelationships,
+        documentPaths,
+        effectFailures,
+        nextActions,
+    };
+}
+// implements REQ-kibi-change-to-proof-plan-compiler-v2
+async function executeCompilePlan(args, context, onCommitted, recovered) {
     validateCompilePlanShape(args);
+    // Re-applying a plan whose interrupted application this call just
+    // completed returns that completion instead of failing its snapshot check.
+    const completed = recovered.find((recovery) => recovery.planHash === args.plan.planHash &&
+        recovery.action === "completed");
+    if (completed !== undefined) {
+        return planJournalRecoveryResult(context, completed, openPlanApplyJournalById(context, completed.journalId).journal);
+    }
     const prolog = context.prolog ?? (await context.ensureProlog?.()) ?? undefined;
     if (!prolog)
         throw new Error("Apply plan requires a Prolog runtime");
@@ -1106,10 +1586,16 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
     // compiled entity steps against the staged source snapshot without asking
     // each step to independently select a document target; otherwise a plan
     // with multiple authored entity kinds could be rejected for an ambiguous
-    // per-entity path after its source batch has already been validated.
-    const operationContext = context.prolog
-        ? { ...context, sourceFirst: false }
-        : { ...context, prolog, sourceFirst: false };
+    // per-entity path after its source batch has already been validated. One
+    // clock reading stamps every step, so the journaled store payload is exactly
+    // what validation produced.
+    const now = context.clock();
+    const operationContext = {
+        ...context,
+        prolog,
+        sourceFirst: false,
+        clock: () => now,
+    };
     const statusResult = await executeStatus({}, operationContext);
     const status = statusResult.structuredContent;
     if (!status)
@@ -1125,77 +1611,55 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
         throw new Error("Apply plan failed: workspace snapshot changed since compilation");
     const sourceHashesChecked = await validateSources(operationContext, args.plan.expected.sourceHashes);
     const steps = args.plan.steps.map((step) => asUpsert(step));
-    const sourceWrites = await applySourceWrites(operationContext, args.plan.sourceWrites, args.plan.planHash, false, onCommitted);
-    const notes = [
-        "Plan steps and tracked source writes are validated before sequential application; source writes are journaled for replay.",
-    ];
-    let changedEntities = 0;
-    let changedRelationships = 0;
-    let appliedSteps = 0;
-    const effectFailures = [];
-    const nextActions = [];
-    let compiledCommit = false;
+    // implements REQ-kibi-truthful-consistency
+    // Run every step through the same validation chain executeUpsert runs,
+    // then stage all of them together in a rolled-back transaction, before the
+    // first write. A step executeUpsert would reject, or a final state that
+    // introduces a contradiction or an infeasible success scenario, fails the
+    // whole plan up front. Limits of the staged emulation:
+    // - symbol granularity reads source code from the workspace as it is now;
+    //   the plan's sourceWrites are validated again once they are published,
+    //   before the store commit, and a failure then rolls them back;
+    // - staged entities are the validated plan payloads; fields executeUpsert
+    //   derives while committing source-first (canonical symbol re-extraction,
+    //   chosen source paths) do not arise, because compile plans apply with
+    //   sourceFirst disabled;
+    // - the store's own checks (entity schema, relationship endpoints,
+    //   requirement contradictions) run again inside the batch transaction, so
+    //   state another writer changed after this preflight aborts the whole
+    //   batch instead of committing part of it.
+    let validated;
     try {
-        for (const step of steps) {
-            const result = await executeUpsert(step, operationContext);
-            appliedSteps += 1;
-            // Each step's compiled commit is an authoritative mutation boundary.
-            // Mark it immediately so a later step's failure can never be mistaken
-            // for a retryable whole-plan failure.
-            onCommitted();
-            const payload = result.structuredContent;
-            if (payload && typeof payload === "object") {
-                const row = payload;
-                changedEntities += Number(row.created ?? 0) + Number(row.updated ?? 0);
-                changedRelationships += Number(row.relationships_created ?? 0);
-                const details = payload;
-                if (Array.isArray(details.effectFailures)) {
-                    effectFailures.push(...details.effectFailures.filter(isRecord));
-                }
-                if (Array.isArray(details.nextActions)) {
-                    nextActions.push(...details.nextActions.filter(isRecord));
-                }
-            }
-        }
-        compiledCommit = true;
-        onCommitted();
+        validated = await validatePlanSteps(steps, operationContext);
     }
     catch (error) {
-        if (sourceWrites.journalId !== null) {
-            effectFailures.push({
-                kind: "compiled-store",
-                errorCode: "DERIVED_COMMIT_FAILED",
-                detail: error instanceof Error ? error.message : String(error),
-            });
-            nextActions.push({
-                operation: "kb_apply_plan",
-                input: { recoveryJournalId: sourceWrites.journalId },
-                reason: "Authoritative source files are committed but compiled effects failed; replay the recovery journal instead of retrying the original mutation.",
-                required: true,
-            });
-            onCommitted();
-            await markSourceJournal(operationContext, sourceWrites.journalId, "repair_required");
-        }
-        else if (appliedSteps > 0) {
-            // A journalless plan (sourceWrites: []) already committed earlier steps
-            // when a later step failed. Expose an explicit non-retryable
-            // partial-commit error instead of a generic exception that invites a
-            // blind retry of the whole plan.
-            if (error instanceof OperationError)
-                throw error;
-            throw new OperationError("PARTIAL_COMMIT_REPAIR_REQUIRED", `Plan ${args.plan.planHash} committed ${appliedSteps} of ${steps.length} step(s) before failing: ${error instanceof Error ? error.message : String(error)}. This plan carries no recovery journal; do not retry the original plan; inspect the committed snapshot and apply a fresh plan for the remaining steps`, false);
-        }
-        else {
-            throw error;
-        }
-    }
-    if (compiledCommit) {
-        await markSourceJournal(operationContext, sourceWrites.journalId, "compiled_published");
+        throw new Error(`Apply plan failed before any write: ${errorMessage(error)}`);
     }
+    const preflight = await prolog.query(planWhatIfGoal(args.plan.steps, now));
+    if (!preflight.success)
+        throw new Error(`Apply plan failed before any write: the store rejected the staged plan: ${preflight.error ?? "unknown error"}`);
+    const staged = parseWhatIfAnalysis(preflight.bindings.JsonString);
+    if (staged === null)
+        throw new Error("Apply plan failed before any write: the staged plan's contradiction analysis could not be read");
+    const introducedBlocking = staged.introduced.filter(isBlockingWitness);
+    if (introducedBlocking.length > 0)
+        throw new Error(`Apply plan failed before any write: the staged plan introduces ${introducedBlocking.length} contradiction(s) or infeasible scenario(s): ${introducedBlocking
+            .map((witness) => witness.reason || witness.requirements.join("/"))
+            .join("; ")}`);
+    const commit = await commitCompilePlan(operationContext, prolog, args.plan, validated, async () => {
+        await validatePlanSteps(steps, operationContext);
+    }, now, onCommitted);
+    const effectFailures = [...commit.effectFailures];
+    const nextActions = [...commit.nextActions];
+    const notes = [
+        commit.journalId === null
+            ? "Plan steps were validated together and committed in one store transaction."
+            : `Plan steps were validated together, journaled in ${commit.journalId}, and committed in one store transaction; source writes are restored from the journal if the commit fails.`,
+    ];
     // Everything before this point is authoritative. A status/workspace
     // readback failure therefore cannot turn the operation into a retryable
-    // mutation: return a repairable partial completion with deterministic next
-    // actions instead.
+    // mutation: return a repairable completion with deterministic next actions
+    // instead.
     let finalStatus;
     let finalWorkspace;
     let postCommitFailure;
@@ -1211,7 +1675,7 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
         }
     }
     catch (error) {
-        postCommitFailure = error instanceof Error ? error.message : String(error);
+        postCommitFailure = errorMessage(error);
         effectFailures.push({
             kind: "post-commit-readback",
             errorCode: "POST_COMMIT_READBACK_FAILED",
@@ -1226,7 +1690,6 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
             reason: "After status is readable, run the consistency checks and follow their typed repair actions.",
             required: true,
         });
-        await markSourceJournal(operationContext, sourceWrites.journalId, "repair_required");
     }
     const finalSnapshots = finalStatus !== undefined && finalWorkspace?.available === true
         ? {
@@ -1243,9 +1706,9 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
         version: PLAN_APPLY_RESULT_VERSION,
         outcome: "applied",
         planHash: args.plan.planHash,
-        changedEntities,
-        changedRelationships,
-        changedPaths: sourceWrites.paths,
+        changedEntities: commit.changedEntities,
+        changedRelationships: commit.changedRelationships,
+        changedPaths: [...commit.documentPaths],
         finalSnapshots,
         validationSummary: {
             stepsValidated: steps.length,
@@ -1253,7 +1716,7 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
             sourceHashesChecked,
             notes,
         },
-        recoveryJournalId: sourceWrites.journalId,
+        recoveryJournalId: commit.journalId,
         ...(effectFailures.length > 0 || postCommitFailure !== undefined
             ? {
                 status: "committed_with_repairs",
@@ -1266,14 +1729,155 @@ async function executeApplyPlanUnlocked(args, context, onCommitted = () => undef
         content: [
             {
                 type: "text",
-                text: `Applied plan ${args.plan.planHash.slice(0, 12)} with ${steps.length} sequential step(s).`,
+                text: `Applied plan ${args.plan.planHash.slice(0, 12)}: ${steps.length} step(s) committed in one store transaction.`,
             },
         ],
         structuredContent: payload,
     };
 }
-// implements REQ-agent-guided-migration-orchestration, REQ-cli-canonical-runtime, REQ-KIBI-BOOTSTRAP-PLAN, REQ-kibi-change-to-proof-plan-compiler, REQ-kibi-predicate-vocabulary-migration
+// implements REQ-kibi-change-to-proof-plan-compiler-v2, REQ-core-atomic-upsert-persistence
+/** The kb_apply_plan result for a plan journal this call recovered or found finished. */
+async function planJournalRecoveryResult(context, recovery, journal) {
+    let finalSnapshots = {
+        branch: journal.branch,
+        kbSnapshotId: "recovered",
+        workspaceSnapshot: "recovered",
+    };
+    try {
+        const status = (await executeStatus({}, context)).structuredContent;
+        const workspace = await readWorkspaceSnapshot(context);
+        if (status !== undefined && workspace.available) {
+            finalSnapshots = {
+                branch: status.branch,
+                kbSnapshotId: status.snapshotId,
+                workspaceSnapshot: workspace.snapshot.hash,
+            };
+        }
+    }
+    catch {
+        // Snapshot readback is informational after a recovery.
+    }
+    const completedNow = recovery.action === "completed";
+    return {
+        content: [{ type: "text", text: recovery.detail }],
+        structuredContent: {
+            version: PLAN_APPLY_RESULT_VERSION,
+            outcome: recovery.state === "committed" ? "replayed" : "rolled_back",
+            planHash: recovery.planHash,
+            changedEntities: completedNow ? journal.summary.changedEntities : 0,
+            changedRelationships: completedNow
+                ? journal.summary.changedRelationships
+                : 0,
+            changedPaths: recovery.restoredPaths,
+            finalSnapshots,
+            validationSummary: {
+                stepsValidated: 0,
+                stepsApplied: completedNow ? journal.summary.changedEntities : 0,
+                sourceHashesChecked: journal.summary.filePaths.length,
+                notes: [recovery.detail],
+            },
+            recoveryJournalId: recovery.journalId,
+            ...(recovery.receiptFailure !== undefined
+                ? {
+                    status: "committed_with_repairs",
+                    effectFailures: [
+                        {
+                            kind: "pending-source-receipt",
+                            errorCode: "PENDING_SOURCE_RECEIPT_FAILED",
+                            detail: recovery.receiptFailure,
+                        },
+                    ],
+                    nextActions: [
+                        {
+                            operation: "kb_apply_plan",
+                            input: { recoveryJournalId: recovery.journalId },
+                            reason: "The plan is committed, but binding its new source files to pending-source receipts failed; recover the journal again to finish them.",
+                            required: true,
+                        },
+                    ],
+                }
+                : {}),
+        },
+    };
+}
+// implements REQ-kibi-change-to-proof-plan-compiler-v2, REQ-core-atomic-upsert-persistence
+async function executePlanJournalRecovery(journalId, context, recovered) {
+    if (!context.fs)
+        throw new Error("Plan journal recovery requires a filesystem-capable runtime");
+    const handle = openPlanApplyJournalById(context, journalId);
+    const recovery = recovered.find((candidate) => candidate.journalId === journalId) ??
+        (await recoverPlanApplyJournal(context, handle, {
+            prolog: async () => context.prolog ?? (await context.ensureProlog?.()),
+        }));
+    return planJournalRecoveryResult(context, recovery, handle.journal);
+}
+/**
+ * Finish every interrupted plan application of the active branch before
+ * this call reads or writes anything.
+ */
+async function recoverInterruptedPlans(context, explicitJournalId) {
+    if (!context.fs)
+        return [];
+    return settlePendingPlanApplyJournals(context, {
+        prolog: async () => context.prolog ?? (await context.ensureProlog?.()),
+    }, explicitJournalId);
+}
+/** Report recoveries this call performed alongside its own result. */
+function withRecoveryReport(result, recovered) {
+    const structured = result.structuredContent;
+    const own = typeof structured.recoveryJournalId === "string"
+        ? structured.recoveryJournalId
+        : undefined;
+    const reported = recovered.filter((recovery) => recovery.action !== "none" && recovery.journalId !== own);
+    if (reported.length === 0)
+        return result;
+    const notes = reported.map((recovery) => recovery.detail);
+    const [first, ...rest] = result.content;
+    const content = [
+        {
+            type: "text",
+            text: [first?.text ?? "", ...notes].join(" ").trim(),
+        },
+        ...rest,
+    ];
+    const recoveredJournals = reported.map((recovery) => ({
+        journalId: recovery.journalId,
+        planHash: recovery.planHash,
+        action: recovery.action,
+        restoredPaths: recovery.restoredPaths,
+    }));
+    if (isRecord(structured.validationSummary)) {
+        const summary = structured.validationSummary;
+        return {
+            content,
+            structuredContent: {
+                ...structured,
+                validationSummary: {
+                    ...summary,
+                    notes: [
+                        ...(Array.isArray(summary.notes) ? summary.notes : []),
+                        ...notes,
+                    ],
+                    recoveredJournals,
+                },
+            },
+        };
+    }
+    if (Array.isArray(structured.notes)) {
+        return {
+            content,
+            structuredContent: {
+                ...structured,
+                notes: [...structured.notes, ...notes],
+            },
+        };
+    }
+    return { content, structuredContent: result.structuredContent };
+}
+// implements REQ-agent-guided-migration-orchestration, REQ-cli-canonical-runtime, REQ-KIBI-BOOTSTRAP-PLAN, REQ-kibi-change-to-proof-plan-compiler-v2, REQ-kibi-predicate-vocabulary-migration
 export async function executeApplyPlan(args, context) {
+    if (isBootstrapApplyArgs(args))
+        preflightBootstrapActions(validateBootstrapPlanShape(args), context);
     if (!context.fs || context.sourceMutationLockHeld === true)
         return executeApplyPlanUnlocked(args, context);
     const lock = await acquireWorkspaceMutationLock(context.workspaceRoot);
@@ -1513,6 +2117,10 @@ async function applyMigrationAction(action, context) {
             await applyPredicateSchemaAlignment(action, context);
             return;
         default:
+            if (SCHEMA6_AUTOMATIC_CODES.has(action.code)) {
+                await applySchema6MigrationAction(action, context);
+                return;
+            }
             throw new Error(`Migration action '${action.code}' has no automatic executor.`);
     }
 }