diff --git a/src/application/AuthorizedArtifactInventory.ts b/src/application/AuthorizedArtifactInventory.ts
index f58641625..7800ed48c 100644
--- a/src/application/AuthorizedArtifactInventory.ts
+++ b/src/application/AuthorizedArtifactInventory.ts
@@ -8,6 +8,7 @@ import {
   type ArtifactIntegrityPolicy,
   type ArtifactInventorySnapshot,
 } from "./ArtifactInventory.js";
+import { canonicalizeConfiguredRoots } from "./ConfiguredRoots.js";
 
 /** Resolve, authorize, and scan one artifact without a second path resolution. */
 export const scanAuthorizedArtifactInventory = async (
@@ -24,7 +25,7 @@ export const scanAuthorizedArtifactInventory = async (
     );
   const [path, approved] = await Promise.all([
     realpath(inputPath),
-    Promise.all(roots.map(async (root) => realpath(root))),
+    canonicalizeConfiguredRoots(roots),
   ]);
   if (!approved.some((root) => withinRoot(root, path)))
     throw new ArtifactReaderFailure(
diff --git a/src/application/BoundedJsonFiles.ts b/src/application/BoundedJsonFiles.ts
index c62c708d9..21e936460 100644
--- a/src/application/BoundedJsonFiles.ts
+++ b/src/application/BoundedJsonFiles.ts
@@ -6,6 +6,7 @@ import writeFileAtomic from "write-file-atomic";
 import type { EvidenceFilePolicy } from "../domain/evidenceBundle.js";
 import { EvidenceFileError } from "../domain/errors.js";
 import { err, ok, type Result } from "../domain/result.js";
+import { canonicalizeConfiguredRoots } from "./ConfiguredRoots.js";
 
 /** Read bounded JSON data from a regular file beneath an approved root. */
 export const readBoundedJson = async (
@@ -82,8 +83,9 @@ const isApproved = async (
   candidate: string,
   roots: readonly string[],
 ): Promise<boolean> => {
-  for (const configuredRoot of roots) {
-    const root = await realpath(resolve(configuredRoot));
+  for (const root of await canonicalizeConfiguredRoots(
+    roots.map((configuredRoot) => resolve(configuredRoot)),
+  )) {
     const relation = relative(root, candidate);
     if (
       relation === "" ||
diff --git a/src/application/ConfiguredRoots.ts b/src/application/ConfiguredRoots.ts
new file mode 100644
index 000000000..b04ede63c
--- /dev/null
+++ b/src/application/ConfiguredRoots.ts
@@ -0,0 +1,22 @@
+import { realpath } from "node:fs/promises";
+
+/** Canonicalize configured policy roots while ignoring stale missing entries. */
+export const canonicalizeConfiguredRoots = async (
+  roots: readonly string[],
+): Promise<string[]> => {
+  const canonical: string[] = [];
+  for (const root of roots) {
+    try {
+      canonical.push(await realpath(root));
+    } catch (cause: unknown) {
+      if (!isMissingPath(cause)) throw cause;
+    }
+  }
+  return canonical;
+};
+
+const isMissingPath = (cause: unknown): boolean =>
+  typeof cause === "object" &&
+  cause !== null &&
+  "code" in cause &&
+  cause.code === "ENOENT";
diff --git a/src/application/ProcessCaptureAuthority.ts b/src/application/ProcessCaptureAuthority.ts
index 9b4041232..74bf6dc4d 100644
--- a/src/application/ProcessCaptureAuthority.ts
+++ b/src/application/ProcessCaptureAuthority.ts
@@ -8,6 +8,7 @@ import {
   ProcessCaptureError,
   processCaptureCancelled,
 } from "./ProcessCaptureError.js";
+import { canonicalizeConfiguredRoots } from "./ConfiguredRoots.js";
 
 const isWithin = (candidate: string, root: string): boolean =>
   candidate === root ||
@@ -18,17 +19,15 @@ export const assertRealPathAuthority = async (
   policy: ProcessExecutionPolicy,
 ): Promise<void> => {
   const executable = await realpath(scenario.executable);
-  const executableRoots = await Promise.all(
-    policy.executableRoots.map((root) => realpath(root)),
+  const executableRoots = await canonicalizeConfiguredRoots(
+    policy.executableRoots,
   );
   if (!executableRoots.some((root) => isWithin(executable, root)))
     throw new ProcessCaptureError(
       "resolved executable is outside approved roots",
     );
   const workingDirectory = await realpath(scenario.working_directory);
-  const workingRoots = await Promise.all(
-    policy.workingRoots.map((root) => realpath(root)),
-  );
+  const workingRoots = await canonicalizeConfiguredRoots(policy.workingRoots);
   if (!workingRoots.some((root) => isWithin(workingDirectory, root)))
     throw new ProcessCaptureError(
       "resolved working directory is outside approved roots",
diff --git a/src/application/ProcessCaptureLifecycle.ts b/src/application/ProcessCaptureLifecycle.ts
index bf1d89bf6..afe98cc5b 100644
--- a/src/application/ProcessCaptureLifecycle.ts
+++ b/src/application/ProcessCaptureLifecycle.ts
@@ -338,14 +338,12 @@ export const captureTerminalFrames = (options: {
   readonly started: number;
   readonly temporaryRoot: string;
   readonly onOutput: () => void;
-  readonly onFirstOutput: () => void;
   readonly renderer: TerminalRenderer;
   readonly checkpoints: ProcessCheckpoints;
 }): (() => boolean) => {
   let outputBytes = 0;
   let truncated = false;
   options.terminal.onData((data) => {
-    options.onFirstOutput();
     options.onOutput();
     const bytes = Buffer.byteLength(data);
     if (
diff --git a/src/application/ProcessHarness.ts b/src/application/ProcessHarness.ts
index 539e6ab08..7cc48b33e 100644
--- a/src/application/ProcessHarness.ts
+++ b/src/application/ProcessHarness.ts
@@ -130,20 +130,6 @@ const scheduleScenarioEvents = (options: ScenarioEventOptions): void => {
   }
 };
 
-const startScenarioEvents = (options: ScenarioEventOptions): (() => void) => {
-  let eventsStarted = false;
-  return () => {
-    if (eventsStarted) return;
-    eventsStarted = true;
-    scheduleScenarioEvents(options);
-  };
-};
-
-const eventsRequireReadiness = (scenario: ProcessScenario): boolean =>
-  scenario.events.some(
-    (event) => event.type === "input" || event.type === "resize",
-  );
-
 interface StartedCaptureRuntime {
   readonly replay: LoopbackReplay;
   readonly renderer: TerminalRenderer;
@@ -243,22 +229,20 @@ const startCaptureRuntime = async (options: {
       rows: scenario.terminal.rows,
       name: "xterm-256color",
     });
-    const startEvents = startScenarioEvents({
-      ...options,
-      getTerminal: () => terminal,
-      renderer,
-      started,
-    });
-    if (!eventsRequireReadiness(scenario)) startEvents();
     const framesTruncated = captureTerminalFrames({
       ...options,
       terminal,
       started,
       onOutput: () => (lastOutput = Date.now()),
-      onFirstOutput: startEvents,
       renderer,
       checkpoints,
     });
+    scheduleScenarioEvents({
+      ...options,
+      getTerminal: () => terminal,
+      renderer,
+      started,
+    });
     const stopSampler = startProcessSampler(
       terminal.pid,
       started,
diff --git a/src/application/ProjectPermissionStore.ts b/src/application/ProjectPermissionStore.ts
index c9876765f..2c52c77dd 100644
--- a/src/application/ProjectPermissionStore.ts
+++ b/src/application/ProjectPermissionStore.ts
@@ -104,9 +104,14 @@ export const readProjectPermissionStore = async (
     const metadata = await stat(path);
     if ((metadata.mode & 0o077) !== 0)
       return err(new ProjectPermissionStoreError("not_owner_only"));
-    const parsed = storeSchema.safeParse(
-      JSON.parse(await readFile(path, "utf8")),
-    );
+    const encoded = await readFile(path, "utf8");
+    let decoded: unknown;
+    try {
+      decoded = JSON.parse(encoded);
+    } catch (cause: unknown) {
+      return err(new ProjectPermissionStoreError("invalid", { cause }));
+    }
+    const parsed = storeSchema.safeParse(decoded);
     if (
       !parsed.success ||
       parsed.data.project_id !== project.value.id ||
diff --git a/src/application/ReferenceSourceImportPolicy.ts b/src/application/ReferenceSourceImportPolicy.ts
index d10a5282d..ca7194420 100644
--- a/src/application/ReferenceSourceImportPolicy.ts
+++ b/src/application/ReferenceSourceImportPolicy.ts
@@ -12,6 +12,7 @@ import {
   type ReferenceSourceImportError,
   type ReferenceSourceImportOptions,
 } from "./ReferenceSourceImportTypes.js";
+import { canonicalizeConfiguredRoots } from "./ConfiguredRoots.js";
 
 /** Validated, authorized inputs ready for filesystem traversal. */
 export interface PreparedReferenceSourceImport {
@@ -66,8 +67,10 @@ const authorizeRoot = async (
         failure("invalid-root", "Reference source root is not a directory"),
       );
     const canonicalRoot = await realpath(resolve(requestedRoot));
-    for (const approvedRoot of approvedRoots) {
-      const canonicalApproved = await realpath(resolve(approvedRoot));
+    const canonicalApprovedRoots = await canonicalizeConfiguredRoots(
+      approvedRoots.map((approvedRoot) => resolve(approvedRoot)),
+    );
+    for (const canonicalApproved of canonicalApprovedRoots) {
       if (withinRoot(canonicalApproved, canonicalRoot))
         return ok(canonicalRoot);
     }
diff --git a/tests/authorizedArtifactInventory.test.ts b/tests/authorizedArtifactInventory.test.ts
new file mode 100644
index 000000000..2cf170ffe
--- /dev/null
+++ b/tests/authorizedArtifactInventory.test.ts
@@ -0,0 +1,34 @@
+import { mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { describe, expect, it } from "vitest";
+
+import { scanAuthorizedArtifactInventory } from "../src/application/AuthorizedArtifactInventory.js";
+
+const LIMITS = {
+  maxEntries: 100,
+  maxTotalBytes: 1024 * 1024,
+  maxEntryBytes: 1024 * 1024,
+  maxCompressionRatio: 100,
+  maxDepth: 10,
+  maxPathBytes: 1024,
+} as const;
+
+describe("authorized artifact inventory", () => {
+  it("uses a valid input root when another configured root is missing", async () => {
+    const root = await mkdtemp(join(tmpdir(), "rea-artifact-roots-"));
+    try {
+      const path = join(root, "artifact.js");
+      await writeFile(path, "export const value = 1;\n");
+      const inventory = await scanAuthorizedArtifactInventory(
+        path,
+        [join(root, "missing"), root],
+        LIMITS,
+      );
+      expect(inventory.manifest.root_format).toBe("javascript-bundle");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+});
diff --git a/tests/evidenceBundleFiles.test.ts b/tests/evidenceBundleFiles.test.ts
index 76ff41694..c98661a3f 100644
--- a/tests/evidenceBundleFiles.test.ts
+++ b/tests/evidenceBundleFiles.test.ts
@@ -93,6 +93,21 @@ describe("evidence bundle filesystem adapter", () => {
     ).toMatchObject({ ok: true });
   });
 
+  it("uses valid evidence roots when another configured root is missing", async () => {
+    directory = await mkdtemp(join(tmpdir(), "rea-evidence-roots-"));
+    const path = join(directory, "bundle.json");
+    const configured = {
+      ...policy(directory),
+      roots: [join(directory, "missing"), directory],
+    };
+    expect(
+      await writeEvidenceBundle(bundle(), path, false, configured),
+    ).toMatchObject({ ok: true });
+    expect(await readEvidenceBundle(path, configured)).toMatchObject({
+      ok: true,
+    });
+  });
+
   it("rejects traversal and symlink escape from approved roots", async () => {
     directory = await mkdtemp(join(tmpdir(), "rea-evidence-"));
     const root = join(directory, "approved");
diff --git a/tests/fixtures/processFidelity.mjs b/tests/fixtures/processFidelity.mjs
index 0d4864845..27227f602 100644
--- a/tests/fixtures/processFidelity.mjs
+++ b/tests/fixtures/processFidelity.mjs
@@ -18,6 +18,13 @@ if (mode === "interactive") {
   process.stdin.on("data", (value) => {
     process.stdout.write(`input:${value.toString()} unicode:雪\n`);
   });
+} else if (mode === "silent-interactive") {
+  process.stdin.setRawMode?.(true);
+  process.stdin.resume();
+  process.stdin.on("data", (value) => {
+    process.stdout.write(`input:${value.toString()}\n`);
+    process.exit(0);
+  });
 } else if (mode === "partial") {
   process.stdout.write("partial-");
   setTimeout(() => {
diff --git a/tests/processCapture.test.ts b/tests/processCapture.test.ts
index db914a9ac..d1b5b3047 100644
--- a/tests/processCapture.test.ts
+++ b/tests/processCapture.test.ts
@@ -1067,6 +1067,47 @@ describe("process capture adapter", () => {
     expect(result.value.exit.code).toBe(0);
   });
 
+  it("dispatches scheduled events before a silent PTY produces output", async () => {
+    const capability = await probeProcessCaptureCapability();
+    if (!capability.available) return;
+    const result = await captureProcessScenario(
+      parseProcessScenario({
+        approved: true,
+        executable: process.execPath,
+        arguments: [processFixture, "silent-interactive"],
+        working_directory: dirname(processFixture),
+        events: [
+          { type: "resize", at_ms: 25, columns: 100, rows: 40 },
+          { type: "input", at_ms: 50, data: "answer" },
+        ],
+        timeout_ms: 2_000,
+        idle_timeout_ms: 2_000,
+      }),
+      {
+        enabled: true,
+        executableRoots: [
+          join(dirname(process.execPath), "missing"),
+          dirname(process.execPath),
+        ],
+        workingRoots: [
+          join(dirname(processFixture), "missing"),
+          dirname(processFixture),
+        ],
+        allowedEnvironment: [],
+        allowExternalNetwork: true,
+      },
+    );
+    expect(result.ok).toBe(true);
+    if (!result.ok) throw result.error;
+    expect(result.value.frames.map(({ data }) => data).join("")).toContain(
+      "input:answer",
+    );
+    expect(result.value.interaction_events).toMatchObject([
+      { type: "resize", outcome: "dispatched" },
+      { type: "input", outcome: "dispatched" },
+    ]);
+  });
+
   it("samples and cleans a source-owned child and grandchild process tree", async () => {
     const capability = await probeProcessCaptureCapability();
     if (!capability.available) return;
diff --git a/tests/projectPermissionStore.test.ts b/tests/projectPermissionStore.test.ts
index 823731934..fbea54278 100644
--- a/tests/projectPermissionStore.test.ts
+++ b/tests/projectPermissionStore.test.ts
@@ -1,4 +1,4 @@
-import { chmod, mkdtemp, stat } from "node:fs/promises";
+import { chmod, mkdtemp, stat, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
@@ -62,6 +62,17 @@ describe("project permission store", () => {
     });
   });
 
+  it("classifies malformed JSON as an invalid store", async () => {
+    const project = await mkdtemp(join(tmpdir(), "rea-policy-invalid-"));
+    const path = join(project, "permissions.json");
+    await writeFile(path, "{", { mode: 0o600 });
+
+    expect(await readProjectPermissionStore(path, project)).toMatchObject({
+      ok: false,
+      error: { reason: "invalid" },
+    });
+  });
+
   it("serializes concurrent grant revocations without losing an update", async () => {
     const project = await mkdtemp(join(tmpdir(), "rea-policy-revoke-"));
     const path = join(project, ".rea", "permissions.json");
diff --git a/tests/referenceSourceImport.test.ts b/tests/referenceSourceImport.test.ts
index b49fa78dc..957387450 100644
--- a/tests/referenceSourceImport.test.ts
+++ b/tests/referenceSourceImport.test.ts
@@ -34,12 +34,16 @@ const fixture = async (parent: string, name: string): Promise<string> => {
   return root;
 };
 
-const importTree = (root: string, approvedRoot: string, signal?: AbortSignal) =>
+const importTree = (
+  root: string,
+  approvedRoot: string | readonly string[],
+  signal?: AbortSignal,
+) =>
   importReferenceSource({
     root,
     caller: "reference-import-test",
     policy: {
-      roots: [approvedRoot],
+      roots: typeof approvedRoot === "string" ? [approvedRoot] : approvedRoot,
       secretPatterns: [".env", ".env.*"],
       ...limits,
     },
@@ -153,6 +157,20 @@ describe("reference source import", () => {
     }
   });
 
+  it("uses a valid reference root when another configured root is missing", async () => {
+    const parent = await mkdtemp(join(tmpdir(), "rea-reference-roots-"));
+    try {
+      const root = await fixture(parent, "tree");
+      const imported = await importTree(root, [
+        join(parent, "missing"),
+        parent,
+      ]);
+      expect(imported).toMatchObject({ ok: true });
+    } finally {
+      await rm(parent, { recursive: true, force: true });
+    }
+  });
+
   it("records bounded local Git state without invoking Git", async () => {
     const parent = await mkdtemp(join(tmpdir(), "rea-reference-git-"));
     try {