feat(workspaces): verify seeds and add managed repair

Replace binary readiness markers with an evidence-bearing seed manifest and enforce a shared validation contract for minimal and full clones. Add an exclusive audited database repair path with recoverable backup, bounded phase diagnostics, and healthy restart validation.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

scripts/__tests__/provision-worktree-self-heal.test.mjs

@@ -137,7 +137,10 @@ test("uses the base CLI when its import graph boots", () => {
   assert.equal(result.status, 0, result.stderr);
   const config = readWorktreeConfig(worktreeCwd);
   assert.equal(config.$meta.source, "fake-cli");
-  assert.ok(fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-pending")));
+  assert.equal(
+    JSON.parse(fs.readFileSync(path.join(worktreeCwd, ".paperclip", "seed-manifest.json"), "utf8")).state,
+    "pending",
+  );
   const initInvocation = readCliInvocations(baseCwd).find(
     (args) => args[0] === "worktree" && args[1] === "init",
   );
@@ -166,7 +169,10 @@ test("falls back to an isolated config when the base CLI cannot boot", () => {
   );
   const env = fs.readFileSync(path.join(worktreeCwd, ".paperclip", ".env"), "utf8");
   assert.match(env, /PAPERCLIP_IN_WORKTREE=true/);
-  assert.ok(fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-pending")));
+  assert.equal(
+    JSON.parse(fs.readFileSync(path.join(worktreeCwd, ".paperclip", "seed-manifest.json"), "utf8")).state,
+    "pending",
+  );
 });
 
 test("repairs an unhealthy base install under the lock and then uses the CLI", (t) => {
@@ -271,7 +277,7 @@ test("runtime provisioning invokes ensure-seeded once and fast-exits after succe
 
   const second = runRuntimeProvision(baseCwd, worktreeCwd);
   assert.equal(second.status, 0, second.stderr);
-  assert.match(second.stderr, /already seeded; skipping/);
+  assert.match(second.stderr, /already seeded.*skipping/);
   const ensureCallsAfterSecond = readCliInvocations(baseCwd)
     .filter((args) => args[0] === "worktree" && args[1] === "ensure-seeded");
   assert.equal(ensureCallsAfterSecond.length, 1);
@@ -290,3 +296,22 @@ test("runtime provisioning leaves seed-pending in place when ensure-seeded fails
   assert.ok(fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-pending")));
   assert.ok(!fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-complete")));
 });
+
+test("runtime provisioning does not trust a truncated verified manifest", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0, ensureExit: 4 });
+  const worktreeCwd = makeTempDir("paperclip-provision-runtime-truncated-");
+  fs.mkdirSync(path.join(worktreeCwd, ".paperclip"), { recursive: true });
+  fs.writeFileSync(path.join(worktreeCwd, ".paperclip", "config.json"), "{}\n");
+  fs.writeFileSync(
+    path.join(worktreeCwd, ".paperclip", "seed-manifest.json"),
+    JSON.stringify({ version: 2, state: "verified" }),
+  );
+
+  const result = runRuntimeProvision(baseCwd, worktreeCwd);
+  assert.equal(result.status, 4, result.stderr);
+  assert.equal(
+    readCliInvocations(baseCwd)
+      .filter((args) => args[0] === "worktree" && args[1] === "ensure-seeded").length,
+    1,
+  );
+});