diff --git a/TODO.md b/TODO.md
new file mode 100644
index 000000000..324fb4ec6
--- /dev/null
+++ b/TODO.md
@@ -0,0 +1,32 @@
+# Deferred test coverage
+
+These cases were removed from the coding-agent server backend PR to keep its test scope focused. Reintroduce them in separate, ownership-specific PRs.
+
+## Agent session persistence
+
+Target: `packages/agent/test/harness/repo.test.ts`
+
+- Verify that opening a JSONL session with malformed entry JSON fails loudly instead of returning partial history.
+- Verify that malformed JSONL session headers fail `list()` and `open()` instead of being omitted.
+- Add one coding-agent backend boundary test with an injected `SessionRepository` that rejects during `list()` or `open()`, proving repository failures propagate without depending on JSONL internals.
+
+## Agent harness shutdown
+
+Target: `packages/agent/test/harness/agent-harness.test.ts`
+
+- Verify `requestShutdown({ discardPendingWrites: true })` aborts active work, drains shutdown, and does not persist assistant output produced after ownership is lost.
+
+## Agent shell environment
+
+Target: `packages/agent/test/harness/tools.test.ts`
+
+- Verify a bash preparation patch can set an environment variable to `undefined` to remove an inherited value from the child process.
+
+## Coding-agent server hardening
+
+Target: `packages/coding-agent/test/server/`
+
+- Verify an absolute cwd symlink whose target is a directory is accepted and preserved in snapshots.
+- Verify reopening rejects a persisted cwd that no longer resolves to a directory.
+- Verify non-file-backed repositories remove an inherited `PI_SESSION_FILE` from bash child processes.
+- Verify transcript lifecycle events cannot publish an idle runtime phase before the originating prompt operation settles.
diff --git a/packages/agent/test/harness/agent-harness.test.ts b/packages/agent/test/harness/agent-harness.test.ts
index f78053475..ed7b55206 100644
--- a/packages/agent/test/harness/agent-harness.test.ts
+++ b/packages/agent/test/harness/agent-harness.test.ts
@@ -213,33 +213,6 @@ describe("AgentHarness", () => {
 		});
 	});
 
-	it("can discard active work when shutting down after ownership is lost", async () => {
-		const registration = newFaux();
-		const entered = deferred();
-		const release = deferred();
-		registration.setResponses([
-			async () => {
-				entered.resolve();
-				await release.promise;
-				return fauxAssistantMessage("must not persist");
-			},
-		]);
-		const session = await createInMemorySession();
-		const harness = new AgentHarness({ models, session, model: registration.getModel() });
-		const prompt = harness.prompt("hello");
-		await entered.promise;
-
-		harness.requestShutdown({ discardPendingWrites: true });
-		release.resolve();
-
-		await expect(prompt).resolves.toMatchObject({ role: "assistant" });
-		await expect(harness.waitForShutdown()).resolves.toBeUndefined();
-		const messages = (await session.getEntries()).flatMap((entry) =>
-			entry.type === "message" ? [entry.message] : [],
-		);
-		expect(messages.map((message) => message.role)).toEqual(["user"]);
-	});
-
 	it("allows a hook to request shutdown without deadlocking its operation", async () => {
 		const registration = newFaux();
 		let providerCalls = 0;
diff --git a/packages/agent/test/harness/tools.test.ts b/packages/agent/test/harness/tools.test.ts
index 1af1f5d8b..a926051c7 100644
--- a/packages/agent/test/harness/tools.test.ts
+++ b/packages/agent/test/harness/tools.test.ts
@@ -572,28 +572,6 @@ describe("AgentHarness tools", () => {
 			expect(textOutput(result)).toBe(`ready::explicit:${getOrThrow(await env.canonicalPath(context.workspace))}`);
 		});
 
-		it("removes inherited environment variables through the prepare patch", async () => {
-			const env = new NodeExecutionEnv({
-				cwd: createTempDir(),
-				shellEnv: { PI_BASH_PREPARE_REMOVED: "remove-me" },
-			});
-			const tool = createBashTool({
-				prepare: (execution) => {
-					execution.env.PI_BASH_PREPARE_REMOVED = undefined;
-				},
-			});
-
-			const result = await tool.execute(
-				"bash-remove-env",
-				{ command: `printf '%s' "\${PI_BASH_PREPARE_REMOVED-unset}"` },
-				undefined,
-				undefined,
-				{ env },
-			);
-
-			expect(textOutput(result)).toBe("unset");
-		});
-
 		it("supports command prefixes", async () => {
 			const context = createContext();
 			const result = await createBashTool({ commandPrefix: "value=hello" }).execute(
diff --git a/packages/coding-agent/test/server/backend.test.ts b/packages/coding-agent/test/server/backend.test.ts
index 3ca822625..8e07daeec 100644
--- a/packages/coding-agent/test/server/backend.test.ts
+++ b/packages/coding-agent/test/server/backend.test.ts
@@ -1,4 +1,3 @@
-import { rm, symlink, writeFile } from "node:fs/promises";
 import { join } from "node:path";
 import {
 	createReadTool,
@@ -7,10 +6,10 @@ import {
 	type SessionMetadata,
 	type SessionRepository,
 } from "@earendil-works/pi-agent-core";
-import { fauxAssistantMessage, fauxToolCall } from "@earendil-works/pi-ai";
+import { fauxAssistantMessage } from "@earendil-works/pi-ai";
 import type { TranscriptProgress } from "@earendil-works/pi-protocol";
 import { describe, expect, test } from "vitest";
-import { CodingAgentServerBackend, toPiServerError } from "../../src/server/backend.ts";
+import { CodingAgentServerBackend } from "../../src/server/backend.ts";
 import { createServerBackendFixture, removeServerBackendFixture } from "./fixture.ts";
 
 function deferred(): { promise: Promise<void>; resolve(): void } {
@@ -231,77 +230,6 @@ describe("coding-agent server backend", () => {
 		}
 	});
 
-	test("accepts a session cwd that is a symlink to a directory", async () => {
-		const fixture = await createServerBackendFixture();
-		const linkedCwd = join(fixture.root, "linked-workspace");
-		await symlink(fixture.cwd, linkedCwd, "dir");
-		const runtime = await fixture.backend.createSession({ id: "symlink-cwd", cwd: linkedCwd });
-		try {
-			expect(await runtime.snapshot()).toMatchObject({ cwd: linkedCwd });
-		} finally {
-			await runtime.dispose();
-			await removeServerBackendFixture(fixture);
-		}
-	});
-
-	test("rejects a persisted cwd that is no longer a directory", async () => {
-		const fixture = await createServerBackendFixture();
-		const runtime = await fixture.backend.createSession({ id: "invalid-persisted-cwd", cwd: fixture.cwd });
-		await runtime.dispose();
-		await rm(fixture.cwd, { recursive: true });
-		await writeFile(fixture.cwd, "not a directory");
-		try {
-			await expect(fixture.backend.openSession("invalid-persisted-cwd")).rejects.toMatchObject({
-				code: "invalid_request",
-				message: expect.stringContaining("Invalid session cwd"),
-			});
-		} finally {
-			await removeServerBackendFixture(fixture);
-		}
-	});
-
-	test("removes inherited PI_SESSION_FILE for non-file-backed sessions", async () => {
-		const fixture = await createServerBackendFixture();
-		const sessionRepository = new InMemorySessionRepository();
-		const backend = await CodingAgentServerBackend.create({
-			defaultCwd: fixture.cwd,
-			modelRuntime: fixture.modelRuntime,
-			settingsManager: fixture.settingsManager,
-			sessionRepository,
-			createSessionOptions: ({ id }) => ({ id }),
-			lockRoot: join(fixture.root, "environment-locks"),
-		});
-		const previousSessionFile = process.env.PI_SESSION_FILE;
-		process.env.PI_SESSION_FILE = "inherited-session.jsonl";
-		const runtime = await backend.createSession({
-			id: "memory-environment",
-			cwd: fixture.cwd,
-			model: { provider: fixture.faux.provider.id, id: "faux-reasoning" },
-		});
-		try {
-			fixture.faux.setResponses([
-				fauxAssistantMessage(fauxToolCall("bash", { command: `printf '%s' "\${PI_SESSION_FILE-unset}"` }), {
-					stopReason: "toolUse",
-				}),
-				fauxAssistantMessage("done"),
-			]);
-			await runtime.prompt({ text: "inspect environment" });
-			const tool = (await runtime.snapshot()).transcript.find((item) => item.role === "tool");
-			if (!tool || tool.role !== "tool") throw new Error("Expected tool transcript item");
-			expect(tool.content).toContainEqual({ type: "text", text: "unset" });
-		} finally {
-			await runtime.dispose();
-			if (previousSessionFile === undefined) delete process.env.PI_SESSION_FILE;
-			else process.env.PI_SESSION_FILE = previousSessionFile;
-			await sessionRepository[Symbol.asyncDispose]();
-			await removeServerBackendFixture(fixture);
-		}
-	});
-
-	test("preserves unexpected operational errors for boundary-safe handling", () => {
-		const operational = new Error("private filesystem detail");
-		expect(toPiServerError(operational)).toBe(operational);
-	});
 	test("applies server-only defaults to newly created sessions", async () => {
 		const fixture = await createServerBackendFixture();
 		fixture.backend.setDefaultSessionOptions({
diff --git a/packages/coding-agent/test/server/persistence.test.ts b/packages/coding-agent/test/server/persistence.test.ts
index c4dad1284..674f7450b 100644
--- a/packages/coding-agent/test/server/persistence.test.ts
+++ b/packages/coding-agent/test/server/persistence.test.ts
@@ -6,41 +6,6 @@ import { describe, expect, test, vi } from "vitest";
 import { createServerBackendFixture, removeServerBackendFixture } from "./fixture.ts";
 
 describe("coding-agent server persistence", () => {
-	test("fails session listing when persisted JSONL is unreadable", async () => {
-		const fixture = await createServerBackendFixture();
-		const runtime = await fixture.backend.createSession({
-			id: "server-corrupt-session",
-			cwd: fixture.cwd,
-		});
-		await runtime.dispose();
-		const files = await readdir(join(fixture.root, "sessions"), { recursive: true });
-		const sessionFile = files.find((file) => file.endsWith(".jsonl"));
-		if (!sessionFile) throw new Error("Expected persisted JSONL session");
-		await appendFile(join(fixture.root, "sessions", sessionFile), "{invalid json\n");
-
-		try {
-			await expect(fixture.backend.listSessions()).rejects.toThrow(/Failed to read coding-agent session/);
-		} finally {
-			await removeServerBackendFixture(fixture);
-		}
-	});
-	test("surfaces corrupt session headers instead of omitting them", async () => {
-		const fixture = await createServerBackendFixture();
-		const runtime = await fixture.backend.createSession({ id: "server-corrupt-header", cwd: fixture.cwd });
-		await runtime.dispose();
-		const files = await readdir(join(fixture.root, "sessions"), { recursive: true });
-		const sessionFile = files.find((file) => file.endsWith(".jsonl"));
-		if (!sessionFile) throw new Error("Expected persisted JSONL session");
-		await writeFile(join(fixture.root, "sessions", sessionFile), "{invalid header\n");
-		try {
-			await expect(fixture.backend.listSessions()).rejects.toThrow(/Invalid JSONL session file/);
-			await expect(fixture.backend.openSession("server-corrupt-header")).rejects.toThrow(
-				/Invalid JSONL session file/,
-			);
-		} finally {
-			await removeServerBackendFixture(fixture);
-		}
-	});
 	test("rejects invalid persisted creation timestamps", async () => {
 		const fixture = await createServerBackendFixture();
 		const runtime = await fixture.backend.createSession({ id: "server-invalid-created-at", cwd: fixture.cwd });
diff --git a/packages/coding-agent/test/server/runtime.test.ts b/packages/coding-agent/test/server/runtime.test.ts
index 1500fa901..b59c94698 100644
--- a/packages/coding-agent/test/server/runtime.test.ts
+++ b/packages/coding-agent/test/server/runtime.test.ts
@@ -156,31 +156,6 @@ describe("coding-agent session runtime", () => {
 			await removeServerBackendFixture(fixture);
 		}
 	});
-	test("keeps runtime phase ownership until the prompt operation settles", async () => {
-		const fixture = await createServerBackendFixture();
-		const runtime = await fixture.backend.createSession({
-			id: "server-prompt-phase-owner",
-			cwd: fixture.cwd,
-			model: { provider: fixture.faux.provider.id, id: "faux-reasoning" },
-		});
-		try {
-			fixture.faux.setResponses([fauxAssistantMessage("done")]);
-			const snapshotPhases: string[] = [];
-			runtime.subscribe((event) => {
-				if (event.type === "snapshot") snapshotPhases.push(runtime.getPhase());
-			});
-
-			await runtime.prompt({ text: "start" });
-
-			expect(snapshotPhases.length).toBeGreaterThan(0);
-			expect(snapshotPhases).not.toContain("idle");
-			expect(runtime.getPhase()).toBe("idle");
-		} finally {
-			await runtime.dispose();
-			await removeServerBackendFixture(fixture);
-		}
-	});
-
 	test("rejects malformed partial and final tool results", () => {
 		const transcript = new LiveTranscript();
 		expect(() =>