pi-profile-switch 0.4.9 → 0.6.0

package/README.md

@@ -2,7 +2,7 @@
 
 [English](README.md) | [中文](README.zh-CN.md)
 
-Named profiles for [Pi](https://github.com/badlogic/pi-mono). A profile is a named capability bundle you define: skills, extensions, MCP servers, tools (including tools exposed by MCP servers and extensions), model defaults, and extra system-prompt instructions. Switch bundles inside a running Pi session — no restart.
+Named profiles for [Pi](https://github.com/badlogic/pi-mono). A profile is a named set of resources you define: skills, extensions, MCP servers, tools (including tools exposed by MCP servers and extensions), model defaults, and extra system-prompt instructions. Switch profiles inside a running Pi session — no restart.
 
 ## Install
 

package/bin/pi-profile.ts

@@ -16,7 +16,7 @@ import { getAgentDir } from "@earendil-works/pi-coding-agent";
 import { ExtensionError } from "../src/extension-discovery.ts";
 import { parseLauncherArgs } from "../src/launcher/args.ts";
 import { UnknownProfileError, resolveInitialProfile } from "../src/launcher/initial-profile.ts";
-import { sweepStaleRuntimeDirs } from "../src/launcher/runtime-cleanup.ts";
+import { sweepStaleInstances } from "../src/launcher/runtime-cleanup.ts";
 import { spawnPi } from "../src/launcher/spawn.ts";
 import { McpConfigError, MissingMcpAdapterError } from "../src/mcp-config.ts";
 import { CatalogError } from "../src/profile-catalog.ts";
@@ -28,7 +28,7 @@ try {
 	const agentDir = getAgentDir();
 	// Fails before spawning when the profile is unknown or cannot activate.
 	// --approve/--no-approve are consumed here as a one-run trust input.
-	const { plan, discovery, projectSettings, projectDir, warnings } = await resolveInitialProfile(args.profile, {
+	const { plan, discovery, projectDir, warnings } = await resolveInitialProfile(args.profile, {
 		agentDir,
 		cwd: process.cwd(),
 		trustOverride: args.trustOverride,
@@ -36,17 +36,21 @@ try {
 	for (const warning of warnings) {
 		console.error(`pi-profile: warning: ${warning}`);
 	}
-	// Stale per-launch runtime dirs (dead pid, or no pid past the grace
-	// window) are swept before this launch materializes its own. Best-effort:
-	// sweep errors never block the launch.
-	await sweepStaleRuntimeDirs(agentDir);
-	const generated = await generateRuntimeDir(plan, { agentDir, discovery, projectSettings, projectDir });
+	// Stale per-launch instance dirs (dead pid, or no pid past the grace
+	// window) are swept before this launch materializes its own. Directories
+	// holding state pi-profile did not generate are kept and reported instead of
+	// deleted (ADR-0010). Best-effort: sweep errors never block the launch.
+	for (const warning of await sweepStaleInstances()) {
+		console.error(`pi-profile: warning: ${warning}`);
+	}
+	const generated = await generateRuntimeDir(plan, { agentDir, discovery, projectDir });
 	process.exitCode = await spawnPi({
 		generated,
 		piArgs: args.piArgs,
-		// Only the default profile keeps trust behavior native (flag re-applied);
-		// named profiles never forward it — the resolver is the trust gatekeeper.
-		trustOverride: plan.filter === "none" ? args.trustOverride : undefined,
+		// Re-applied for every profile: the one-run trust input must decide both
+		// the resolver's project reads and Pi's project-scope visibility — two
+		// different answers in one launch would be a divergence, not a policy.
+		trustOverride: args.trustOverride,
 	});
 } catch (error) {
 	// Launcher input/selection failures (unknown profile, unresolvable

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pi-profile-switch",
-  "version": "0.4.9",
+  "version": "0.6.0",
   "description": "Named profiles for Pi: reference skills, extensions, MCP servers, and tools per workflow, switched without restarting. Install: npm install -g pi-profile-switch (not pi install).",
   "type": "module",
   "keywords": [

package/src/extension-discovery.ts

@@ -1,6 +1,6 @@
 /**
  * ExtensionDiscovery: implicit, read-only discovery of selectable extensions
- * (ADR-0006/0007), so profiles can reference extensions without any
+ * (ADR-0007/0008), so profiles can reference extensions without any
  * registration step.
  *
  * Two implicit sources, both resolved by Pi itself:

package/src/launcher/initial-profile.ts

@@ -31,7 +31,7 @@ export class UnknownProfileError extends Error {
 	}
 }
 
-/** Zero-match glob references surface as launch warnings (ADR-0006):
+/** Zero-match glob references surface as launch warnings (ADR-0009):
  *  visible, but never blocking — globs re-expand on every resolution. */
 function unmatchedWarnings(plan: ActivationPlan): string[] {
 	return (plan.unmatched ?? []).map(
@@ -53,9 +53,6 @@ export interface InitialProfile {
 	/** Full discovery results for the settings generator. Undefined for the
 	 *  default profile (which applies no filtering). */
 	discovery?: LauncherDiscovery;
-	/** The trusted project's `.pi/settings.json` content, when trusted and
-	 *  present. The generator merges it into the base for selection plans. */
-	projectSettings?: Record<string, unknown>;
 	/** The trusted project directory, when trusted. */
 	projectDir?: string;
 	/** Non-fatal notices for the user (e.g. a dangling restored profile that
@@ -63,13 +60,12 @@ export interface InitialProfile {
 	warnings: string[];
 }
 
-/** Reads the real global `defaultProjectTrust` setting (a trust input) and,
- *  when trusted, the project's `.pi/settings.json`. Exported for the
- *  session-side surfaces (selector/list/status) that need the same trust
- *  gate the launcher uses. */
+/** Reads the real global `defaultProjectTrust` setting (a trust input) and
+ *  resolves the project trust decision from Pi's own trust store. Exported
+ *  for the session-side surfaces (selector/list/status) that need the same
+ *  trust gate the launcher uses. */
 export async function readTrustInputs(context: LauncherContext): Promise<{
 	projectTrusted: boolean;
-	projectSettings?: Record<string, unknown>;
 }> {
 	const globalSettingsPath = path.join(context.agentDir, "settings.json");
 	const globalSettings = await readJsonFile(globalSettingsPath);
@@ -86,10 +82,9 @@ export async function readTrustInputs(context: LauncherContext): Promise<{
 	if (!projectTrusted) {
 		return { projectTrusted };
 	}
-	const projectSettingsResult = await readJsonFile(path.join(context.cwd, ".pi", "settings.json"));
-	const projectSettings =
-		projectSettingsResult.ok && isRecord(projectSettingsResult.value) ? projectSettingsResult.value : undefined;
-	return { projectTrusted, projectSettings };
+	// The project's own `.pi/settings.json` is Pi's to read (natively, for the
+	// same trust decision): pi-profile neither merges nor narrows it.
+	return { projectTrusted };
 }
 
 export async function resolveInitialProfile(
@@ -97,7 +92,7 @@ export async function resolveInitialProfile(
 	context: LauncherContext,
 	options?: { overlay?: RuntimeOverlay },
 ): Promise<InitialProfile> {
-	const { projectTrusted, projectSettings } = await readTrustInputs(context);
+	const { projectTrusted } = await readTrustInputs(context);
 	const projectDir = projectTrusted ? context.cwd : undefined;
 	const catalog = await ProfileCatalog.load(context.agentDir, { projectDir });
 
@@ -156,7 +151,7 @@ export async function resolveInitialProfile(
 			overlay,
 		});
 		warnings.push(...discovery.extensions.warnings(), ...unmatchedWarnings(plan));
-		return { plan, discovery, projectSettings, projectDir, warnings };
+		return { plan, discovery, projectDir, warnings };
 	}
 
 	const discovery = await discoverLauncherResources({ ...context, projectTrusted });
@@ -177,5 +172,5 @@ export async function resolveInitialProfile(
 		// silently do nothing or leak through unfiltered.
 		throw new MissingMcpAdapterError(plan.profile);
 	}
-	return { plan, discovery, projectSettings, projectDir, warnings };
+	return { plan, discovery, projectDir, warnings };
 }

package/src/launcher/runtime-cleanup.ts

@@ -1,35 +1,54 @@
 /**
- * RuntimeCleanup: sweeps stale per-launch runtime directories at startup.
+ * InstanceCleanup: sweeps stale per-launch instance directories at startup.
  *
- * The generated agent dirs under `<agentDir>/pi-profile/runtime/launch-*`
- * (ADR-0005) would otherwise accumulate forever. Startup sweep is the ONLY
- * cleanup mechanism by design: any exit — graceful, signal, SIGKILL, power
- * loss — kills the child pid, so the next launch's sweep converges. There is
- * no exit-time deletion; it would only buy immediacy at the cost of deletion
- * logic on the signal path.
+ * Every launch materializes its own instance dir under
+ * `<PI_PROFILE_SWITCH_DIR>/instances/launch-*` (ADR-0010), which would
+ * otherwise accumulate forever. Startup sweep is the ONLY cleanup mechanism by
+ * design: any exit — graceful, signal, SIGKILL, power loss — kills the child
+ * pid, so the next launch's sweep converges. There is no exit-time deletion; it
+ * would only buy immediacy at the cost of deletion logic on the signal path.
  *
- * Liveness token: a `pid` file written by spawnPi into the runtime dir.
- * (Naming the dir after the pid is impossible — the pid does not exist
- * before spawn, and the running process's PI_CODING_AGENT_DIR path is
- * frozen.) Rules per launch-* dir:
+ * Liveness token: a `pid` file written by spawnPi into the instance dir.
+ * (Naming the dir after the pid is impossible — the pid does not exist before
+ * spawn, and the running process's PI_CODING_AGENT_DIR path is frozen.) Rules
+ * per instance dir:
  * - pid file parses and the process is alive (or EPERM) → keep;
- *   ESRCH → delete.
- * - no/unparsable pid file → delete only when the dir mtime is older than
+ *   ESRCH → candidate.
+ * - no/unparsable pid file → candidate only when the dir mtime is older than
  *   NO_PID_GRACE_MS. The grace window guards the concurrent-launch race (a
- *   second launcher between mkdtemp and its pid write must not be reaped);
- *   it also covers pre-feature dirs and post-mkdtemp crashes.
+ *   second launcher between mkdir and its pid write must not be reaped); it
+ *   also covers post-mkdir crashes.
  * PID reuse needs no /proc check: a wrong keep only delays cleanup and
  * self-heals once the reused pid dies.
  *
+ * A candidate is deleted only when every entry in it is pi-profile's own: a
+ * symlink (the mirror's link into the real agent dir) or a managed generated
+ * file. Anything else is state an extension created at runtime, so the
+ * directory is kept and reported — the sweep never destroys data it cannot
+ * attribute. The check deliberately does NOT consult the real agent dir: a
+ * same-named entry there (a seeded `missions`, say) must not turn an
+ * instance-local real directory into a deletable one.
+ *
  * Everything is best-effort: sweep errors never block a launch.
  */
 
-import { readdir, readFile, rm, stat } from "node:fs/promises";
+import type { Dirent } from "node:fs";
+import { lstat, readdir, readFile, rm, stat } from "node:fs/promises";
 import path from "node:path";
 
-/** Grace period for launch dirs without a (parseable) pid file. */
+import { MANAGED_INSTANCE_FILES } from "../settings-generator.ts";
+import { getInstancesRootDir } from "../workspace.ts";
+
+/** Prefix of the directories this module owns under the instances root. */
+const INSTANCE_DIR_PREFIX = "launch-";
+
+/** Grace period for instance dirs without a (parseable) pid file. */
 export const NO_PID_GRACE_MS = 10 * 60 * 1000;
 
+/** Managed directories whose contents are not necessarily generated: a package
+ *  may write its own files inside them (e.g. an extension's own config). */
+const MANAGED_DIRS_WITH_RUNTIME_CONTENT = new Set(["extensions"]);
+
 function isProcessAlive(pid: number): boolean {
 	try {
 		process.kill(pid, 0);
@@ -40,11 +59,47 @@ function isProcessAlive(pid: number): boolean {
 	}
 }
 
-function runtimeRootOf(agentDir: string): string {
-	return path.join(agentDir, "pi-profile", "runtime");
+/** Paths inside `dir` that pi-profile did not generate, relative to `dir`.
+ *  `undefined` means the directory could not be inspected — the caller must
+ *  treat that as unrecognized rather than as empty. */
+async function unrecognizedEntries(dir: string): Promise<string[] | undefined> {
+	let entries: Dirent<string>[];
+	try {
+		entries = await readdir(dir, { withFileTypes: true });
+	} catch {
+		return undefined;
+	}
+
+	const found: string[] = [];
+	for (const entry of entries) {
+		const entryPath = path.join(dir, entry.name);
+		let linkStat;
+		try {
+			linkStat = await lstat(entryPath);
+		} catch {
+			continue; // Vanished under us: nothing to protect.
+		}
+		// Symlinks only point at the real agent dir and hold no data of their own.
+		if (linkStat.isSymbolicLink()) continue;
+		if (!MANAGED_INSTANCE_FILES.has(entry.name)) {
+			found.push(entry.name);
+			continue;
+		}
+		if (MANAGED_DIRS_WITH_RUNTIME_CONTENT.has(entry.name) && linkStat.isDirectory()) {
+			const nested = await unrecognizedEntries(entryPath);
+			if (nested === undefined) {
+				found.push(entry.name);
+				continue;
+			}
+			found.push(...nested.map((name) => path.join(entry.name, name)));
+		}
+	}
+	return found;
 }
 
-async function sweepEntry(dir: string): Promise<void> {
+/** Reclaims `dir` if it is both dead and free of unrecognized entries.
+ *  Returns the warnings for the cases where it was intentionally kept. */
+async function sweepEntry(dir: string): Promise<string[]> {
 	let pid: number | undefined;
 	try {
 		const raw = await readFile(path.join(dir, "pid"), "utf8");
@@ -55,31 +110,56 @@ async function sweepEntry(dir: string): Promise<void> {
 	}
 
 	if (pid !== undefined) {
-		if (!isProcessAlive(pid)) await rm(dir, { recursive: true, force: true });
-		return;
+		if (isProcessAlive(pid)) return [];
+	} else {
+		const info = await stat(dir);
+		if (Date.now() - info.mtimeMs <= NO_PID_GRACE_MS) return [];
 	}
 
-	const info = await stat(dir);
-	if (Date.now() - info.mtimeMs > NO_PID_GRACE_MS) {
-		await rm(dir, { recursive: true, force: true });
+	const unrecognized = await unrecognizedEntries(dir);
+	if (unrecognized === undefined) {
+		return [
+			`${dir} was not reclaimed: it could not be inspected (permissions?). Check its contents and delete it manually.`,
+		];
 	}
+	if (unrecognized.length > 0) {
+		return [
+			`${dir} was not reclaimed: it holds state pi-profile did not generate (${unrecognized.join(", ")}). ` +
+				`Move that state into the real agent dir (it is mirrored on the next launch), or point the extension that ` +
+				`created it at a fixed path via that extension's own configuration, then delete ${dir}.`,
+		];
+	}
+
+	await rm(dir, { recursive: true, force: true });
+	return [];
 }
 
-/** Deletes stale launch dirs under the agent dir's runtime root. Never throws. */
-export async function sweepStaleRuntimeDirs(agentDir: string): Promise<void> {
+/** Deletes stale instance dirs under the instances root and returns the
+ *  warnings for directories it deliberately kept. Never throws. */
+export async function sweepStaleInstances(): Promise<string[]> {
+	const warnings: string[] = [];
+	const root = getInstancesRootDir();
+
 	let entries: string[];
 	try {
-		entries = await readdir(runtimeRootOf(agentDir));
+		entries = await readdir(root);
 	} catch {
-		return; // No runtime root yet: nothing to sweep.
+		return warnings; // No instances root yet: nothing to sweep.
 	}
+
 	for (const entry of entries) {
-		if (!entry.startsWith("launch-")) continue;
-		const dir = path.join(runtimeRootOf(agentDir), entry);
+		// Only directories this module generated are candidates. Anything else
+		// under the root — 0.4.x's per-profile dirs included — is not ours to
+		// delete, and is left alone without a warning.
+		if (!entry.startsWith(INSTANCE_DIR_PREFIX)) continue;
+		const dir = path.join(root, entry);
 		try {
-			if ((await stat(dir)).isDirectory()) await sweepEntry(dir);
+			if (!(await stat(dir)).isDirectory()) continue;
+			warnings.push(...(await sweepEntry(dir)));
 		} catch {
 			// Best-effort: one bad entry must not stop the sweep or the launch.
 		}
 	}
+
+	return warnings;
 }

package/src/launcher/spawn.ts

@@ -29,7 +29,8 @@ const EXTENSION_ENTRY = fileURLToPath(new URL("../../extensions/pi-profile/index
  *  trust re-application, then user args verbatim. */
 export function buildPiArgs(options: SpawnPiOptions): string[] {
 	const args = ["-e", EXTENSION_ENTRY];
-	// default profile keeps trust behavior native: re-apply the recorded flag.
+	// Re-apply the recorded one-run trust input for every profile: the same input
+	// decided the launcher's project reads, so Pi must decide the same way.
 	if (options.trustOverride === true) args.push("--approve");
 	if (options.trustOverride === false) args.push("--no-approve");
 	args.push(...options.piArgs);

package/src/mcp-config.ts

@@ -40,6 +40,9 @@ export interface McpDiscoveryOptions {
 export interface MergedMcpResult {
 	servers: Record<string, Record<string, unknown>>;
 	sharedServers: Set<string>;
+	/** Servers defined in a trusted project's own config (`.mcp.json`,
+	 *  `.pi/mcp.json`). They are not the profile's to narrow. */
+	projectServers: Set<string>;
 	baseConfig?: Record<string, unknown>;
 }
 
@@ -47,6 +50,9 @@ export interface McpConfigSource {
 	path: string;
 	isShared: boolean;
 	isAgentDir?: boolean;
+	/** Project-scope source: only read for a trusted project, and its servers
+	 *  stay enabled regardless of a profile's `mcps` declaration. */
+	isProject?: boolean;
 }
 
 /**
@@ -71,8 +77,8 @@ export function getStandardMcpConfigSources(
 		{ path: path.join(agentDir, "mcp.json"), isShared: false, isAgentDir: true },
 	];
 	if (projectDir !== undefined) {
-		sources.push({ path: path.join(projectDir, ".mcp.json"), isShared: true });
-		sources.push({ path: path.join(projectDir, ".pi", "mcp.json"), isShared: false });
+		sources.push({ path: path.join(projectDir, ".mcp.json"), isShared: true, isProject: true });
+		sources.push({ path: path.join(projectDir, ".pi", "mcp.json"), isShared: false, isProject: true });
 	}
 	return sources;
 }
@@ -86,6 +92,7 @@ export async function loadMergedMcpServers(
 	const seenPaths = new Set<string>();
 	const servers: Record<string, Record<string, unknown>> = {};
 	const sharedServers = new Set<string>();
+	const projectServers = new Set<string>();
 	let baseConfig: Record<string, unknown> | undefined;
 
 	for (const source of sources) {
@@ -112,6 +119,9 @@ export async function loadMergedMcpServers(
 			if (source.isShared) {
 				sharedServers.add(name);
 			}
+			if (source.isProject === true) {
+				projectServers.add(name);
+			}
 			if (isRecord(def)) {
 				servers[name] = { ...(servers[name] ?? {}), ...def };
 			} else {
@@ -120,7 +130,7 @@ export async function loadMergedMcpServers(
 		}
 	}
 
-	return { servers, sharedServers, baseConfig };
+	return { servers, sharedServers, projectServers, baseConfig };
 }
 
 /** Server names the adapter would discover: standard global MCP configs,

package/src/project-trust.ts

@@ -1,27 +1,31 @@
 /**
- * Project trust resolution for the launcher — pi-profile is the sole
- * gatekeeper for project resources, because generated settings carry
- * `defaultProjectTrust: "never"` and Pi therefore never auto-discovers them.
+ * Project trust resolution for the launcher — pi-profile's gate for the
+ * project-scope content it reads itself: the project catalog, the project
+ * runtime state, and the project MCP config. Project-level resources
+ * (skills, extensions, prompts, themes, settings) are Pi's own business: its
+ * trust store decision, exposed through the linked `trust.json`, decides
+ * their visibility (see ADR-0011).
  *
  * Mirrors Pi's own trust decision order (`resolveProjectTrusted`), with
  * pi-profile's catalog/state files added to the trust-requiring
  * resource set (they are pi-profile's project attack surface; Pi doesn't
  * know about them):
  *   1. one-run `--approve` / `--no-approve` override (consumed by the
- *      launcher, never forwarded for named profiles)
+ *      launcher and re-applied to the spawned pi for every profile)
  *   2. a project with no trust-requiring resources at all is trusted —
  *      there is nothing project-scoped to gate
  *   3. the stored decision in the real `trust.json` (nearest ancestor wins)
  *   4. the user's `defaultProjectTrust` setting — but only "always" grants;
  *      "ask" cannot prompt here (the launcher has no trust UI), so it falls
  *      through to untrusted
- *   5. otherwise untrusted: project catalogs, registries, resources, and
- *      state files are not read at all
+ *   5. otherwise untrusted: project catalogs, project state, and project MCP
+ *      config are not read at all
  *
  * Known divergence from Pi: extension `project_trust` event handlers are not
  * consulted — that would require executing extension code in the launcher,
- * which pi-profile never does. In named-profile sessions the event is moot
- * anyway (generated settings carry `defaultProjectTrust: "never"`).
+ * which pi-profile never does. A spawned Pi still runs those handlers with
+ * its own settings, so an extension that answers yes/no can decide the
+ * project scope of that session.
  */
 
 import { existsSync, readFileSync } from "node:fs";

package/src/settings-generator.ts

@@ -3,9 +3,9 @@
  * runtime directory (ADR-0005).
  *
  * Two entry points:
- * - `generateRuntimeDir` (launcher): mkdtemp a fresh runtime dir, write the
- *   files, link state (auth/models/mcp/npm/git/bin; trust.json only for
- *   default), derive env.
+ * - `generateRuntimeDir` (launcher): create a fresh per-launch runtime dir
+ *   under the workspace instances root, write the files, mirror the real
+ *   agent dir as symlinks (trust.json only for default), derive env.
  * - `writeRuntimeFiles` (in-session switch, ticket 05): rewrite
  *   settings.json + pi-profile.json inside the EXISTING runtime dir (the
  *   running process's PI_CODING_AGENT_DIR cannot move), and transition the
@@ -17,18 +17,20 @@
  * the spawned pi behaves exactly like native `pi`.
  *
  * For named profiles the generated settings encode the profile's selection
- * per the filtering model (see docs/architecture/overview.md):
+ * over user-scope resources only (see docs/architecture/overview.md):
  * - agentDir-scope resources: additive allowlist paths (the discovery root
  *   moved, so nothing auto-discovered from the real agent dir)
  * - `~/.agents` skills: always auto-discovered, so unselected ones are
  *   force-excluded with `-<path>` entries
  * - packages: user-configured package entries rewritten to object form with
  *   per-type allowlists (unmanaged types keep the user's key or Pi's default)
- * - `defaultProjectTrust: "never"` suppresses all project auto-discovery
- *   (project resources enter only through the trust-gated resolver)
- * - project `packages` are stripped from the settings merge (project
- *   packages are unsupported — the key would install into the global npm
- *   root as a launch side effect)
+ * - project-scope resources (project `.pi/skills`, project `.pi/extensions`,
+ *   ancestor `.agents/skills`) are never encoded: Pi discovers them natively
+ *   whenever the project is trusted, and the profile neither adds nor
+ *   excludes them
+ * - `defaultProjectTrust: "never"` only suppresses Pi's interactive trust
+ *   prompt (a stored decision in the real trust.json still applies); the
+ *   project's `.pi/settings.json` is not merged here — Pi reads it natively
  * - unmanaged kinds (prompts, themes) pass through: the user's arrays are
  *   preserved and the real agent dir's prompts/themes dirs re-included
  * - tools/model are written to generated settings (defaultTools,
@@ -74,11 +76,6 @@ export interface GenerateOptions {
 	projectDir?: string;
 	/** Required for selection plans; unused for the default profile. */
 	discovery?: DiscoveryContext;
-	/** The trusted project's `.pi/settings.json` content (already parsed).
-	 *  Only pass when the resolver's trust check passed; merged into the
-	 *  generated base per Pi's merge rules for selection plans. Ignored for
-	 *  the default profile (Pi reads project settings natively there). */
-	projectSettings?: Record<string, unknown>;
 }
 
 export interface GeneratedRuntime {
@@ -99,6 +96,24 @@ export const MANAGED_INSTANCE_FILES = new Set([
 	"extensions",
 ]);
 
+/** State directories that Pi and its extensions resolve under the agent dir,
+ *  and which therefore appear at runtime rather than at install time. They are
+ *  seeded in the REAL agent dir before mirroring, so the instance gets a
+ *  symlink instead of a private real directory: runtime-created state then
+ *  lands where native Pi puts it, and third-party records never embed an
+ *  instance path (ADR-0010). Adding a name here needs observed evidence that a
+ *  package creates that directory under the agent dir; anything unlisted shows
+ *  up as an unrecognized entry in the sweep (src/launcher/runtime-cleanup.ts). */
+const SEEDED_STATE_DIRS = ["sessions", "missions"] as const;
+
+/** State FILES Pi creates at runtime (same evidence rule as the dirs). They
+ *  cannot be created up front — the content is Pi's, not pi-profile's — so the
+ *  instance gets a symlink into the real agent dir that is deliberately allowed
+ *  to dangle: Pi sees no file, writes through the link, and the real agent dir
+ *  gets the file. A real file left here instead would be unrecognized state and
+ *  would strand credentials in a directory the sweep refuses to delete. */
+const SEEDED_STATE_FILES = ["auth.json", "models-store.json"] as const;
+
 /** Resource dirs rooted at the real agent dir, re-included for the default
  *  profile because PI_CODING_AGENT_DIR moves the discovery root. */
 const RESOURCE_DIR_KINDS = ["skills", "extensions", "prompts", "themes"] as const;
@@ -132,21 +147,6 @@ function toPosix(filePath: string): string {
 	return filePath.split(path.sep).join("/");
 }
 
-/** Mirrors Pi's own deepMergeSettings: plain objects merge recursively,
- *  everything else (arrays, primitives) is replaced by the override. */
-function deepMergeSettings(base: Record<string, unknown>, overrides: Record<string, unknown>): Record<string, unknown> {
-	const result: Record<string, unknown> = { ...base };
-	for (const [key, overrideValue] of Object.entries(overrides)) {
-		if (overrideValue === undefined) continue;
-		const baseValue = result[key];
-		result[key] =
-			isRecord(baseValue) && isRecord(overrideValue)
-				? deepMergeSettings(baseValue, overrideValue)
-				: overrideValue;
-	}
-	return result;
-}
-
 function tryRealpath(p: string): string {
 	try {
 		return realpathSync(p);
@@ -176,27 +176,28 @@ function buildSelectionSettings(
 	agentDir: string,
 	discovery: DiscoveryContext,
 	runtimeDir: string,
+	projectDir?: string,
 ): Record<string, unknown> {
 	const settings = { ...userSettings };
 
 	// --- skills ---
-	// Project-scope selections are emitted before user-scope ones: Pi's
-	// same-name collision rule is first-wins, and project resources must keep
-	// their native priority (ticket 03).
-	const orderedSelectedSkills = [...plan.skills].sort((a, b) => {
-		const aProject = a.scope === "project" ? 0 : 1;
-		const bProject = b.scope === "project" ? 0 : 1;
-		return aProject - bProject;
-	});
+	// Only user-scope entries are encoded. Project-scope selections are
+	// skipped below: their visibility is Pi's, so the order they would have
+	// been emitted in carries no meaning.
 	const selectedPaths = new Set(plan.skills.map((skill) => skill.filePath));
 	const skillEntries: string[] = [];
-	for (const skill of orderedSelectedSkills) {
+	for (const skill of plan.skills) {
 		if (skill.origin === "package") continue; // encoded in the packages allowlist
+		// Project scope belongs to Pi: a trusted project's skills are discovered
+		// natively, so selecting one here would duplicate it and excluding one
+		// would contradict the profile's boundary.
+		if (skill.scope === "project") continue;
 		if (isUnderPath(skill.filePath, homeAgentsSkillsDir())) continue; // auto-discovered anyway
 		skillEntries.push(skill.filePath);
 	}
 	for (const skill of discovery.skills) {
 		if (skill.origin === "package") continue;
+		if (skill.scope === "project") continue;
 		if (selectedPaths.has(skill.filePath)) continue;
 		
 		// If the skill is in the real agentDir, Pi will discover it via the symlink.
@@ -222,7 +223,13 @@ function buildSelectionSettings(
 		.map((pkg) => ({ ...pkg, root: pkg.root }));
 	const packageExtensions = new Map<string, string[]>();
 	const extensionEntries: string[] = [];
+	const projectExtensionsDir =
+		projectDir !== undefined ? path.join(projectDir, ".pi", "extensions") : undefined;
 	for (const extension of plan.extensions) {
+		// Loose project extensions are discovered natively by Pi; an explicit
+		// path reference inside the project (outside `.pi/extensions`) is the
+		// profile's own selection and stays.
+		if (projectExtensionsDir !== undefined && isUnderPath(extension.entry, projectExtensionsDir)) continue;
 		const owner = packageRoots.find((pkg) => isUnderPath(extension.entry, pkg.root));
 		if (owner === undefined) {
 			extensionEntries.push(extension.entry);
@@ -298,8 +305,6 @@ export interface RuntimeFileOptions {
 	projectDir?: string;
 	/** Required for selection plans; unused for the default profile. */
 	discovery?: DiscoveryContext;
-	/** The trusted project's `.pi/settings.json` content (already parsed). */
-	projectSettings?: Record<string, unknown>;
 	/** Extra launch-plan fields written by the in-session switch path:
 	 *  `switchedFrom` triggers the one-shot change summary; `persistSelection`
 	 *  tells the post-reload extension instance to save the selection;
@@ -345,21 +350,20 @@ async function computeSettings(
 		return settings;
 	}
 
-	// Selection plans: the trusted project's settings merge into the base
-	// per Pi's merge rules (project wins, nested objects merge), then the
-	// filtering encoding replaces the managed keys on top. With
-	// defaultProjectTrust: "never", Pi itself never reads project settings.
-	//
-	// The project's `packages` key is stripped: project packages install
-	// under the project's .pi/npm and are unreferenceable in generated
-	// global-scope settings — merging the key would make Pi install them
-	// into the (symlinked) global npm root as a launch side effect.
-	let base = { ...userSettings };
-	if (options.projectSettings !== undefined) {
-		const { packages: _stripped, ...mergeable } = options.projectSettings;
-		base = deepMergeSettings(base, mergeable);
-	}
-	return buildSelectionSettings(plan, base, agentDir, options.discovery ?? { skills: [], packages: [] }, runtimeDir);
+	// Selection plans: only user-scope encoding is layered onto the user's own
+	// settings. The trusted project's `.pi/settings.json` is deliberately NOT
+	// merged here — Pi reads it natively for the same trust decision this
+	// process's Pi applies, and merging it would turn the project's `packages`
+	// into global-scope packages (installing them into the real agent dir's npm
+	// root as a launch side effect).
+	return buildSelectionSettings(
+		plan,
+		{ ...userSettings },
+		agentDir,
+		options.discovery ?? { skills: [], packages: [] },
+		runtimeDir,
+		options.projectDir,
+	);
 }
 
 /** Resolved name sets, carried in the launch plan for glob-delta reporting. */
@@ -371,10 +375,9 @@ export interface ResolvedNames {
 }
 
 /** Writes settings.json + pi-profile.json into an existing runtime dir and
- *  transitions the trust.json link to the plan's filter mode: linked for
- *  `default` (native trust behavior), absent for named profiles (a stored
- *  trust decision would beat the generated `defaultProjectTrust: "never"`
- *  inside Pi and re-enable unfiltered project auto-discovery). */
+ *  keeps the trust.json link in place for every profile: Pi reads its
+ *  project-scope decision from that path, and project-level resources belong
+ *  to Pi's trust gate rather than to the profile. */
 export async function writeRuntimeFiles(
 	runtimeDir: string,
 	plan: ActivationPlan,
@@ -405,7 +408,7 @@ export async function writeRuntimeFiles(
 					skills: plan.skills.map((skill) => ({ name: skill.name, filePath: skill.filePath })),
 					extensions: plan.extensions,
 				},
-				// Zero-match glob references (ADR-0006) — surfaced by /profile status
+				// Zero-match glob references (ADR-0009) — surfaced by /profile status
 				// so a typo'd glob is visible instead of silently selecting nothing.
 				...(plan.unmatched !== undefined ? { unmatched: plan.unmatched } : {}),
 				...options.planExtras,
@@ -415,18 +418,14 @@ export async function writeRuntimeFiles(
 		)}\n`,
 	);
 
+	// Every profile gets the link, dangling allowed: Pi's stored trust decision
+	// is what makes a trusted project's resources visible, and a decision Pi
+	// writes through the link must land in the real agent dir (same shape as the
+	// auth.json seed in ADR-0010). An entry that already exists is left alone —
+	// a real file Pi wrote during this session carries its own decision.
 	const trustLink = path.join(runtimeDir, "trust.json");
-	const trustTarget = path.join(options.agentDir, "trust.json");
-	if (plan.filter === "none") {
-		if ((await exists(trustTarget)) && !(await existsLexical(trustLink))) {
-			await symlink(trustTarget, trustLink);
-		}
-	} else if (await existsLexical(trustLink)) {
-		// Lexical check: a dangling trust.json symlink (real trust.json deleted
-		// after the link was made) must still be removed — otherwise a later
-		// re-created real trust.json silently resurrects stored trust inside a
-		// named profile, defeating defaultProjectTrust: "never".
-		await rm(trustLink);
+	if (!(await existsLexical(trustLink))) {
+		await symlink(path.join(options.agentDir, "trust.json"), trustLink);
 	}
 
 	// MCP Servers generation (Ticket 04)
@@ -441,7 +440,7 @@ export async function writeRuntimeFiles(
 	} else {
 		// Filter MCP servers
 		try { await rm(mcpInstancePath); } catch {}
-		const { servers, sharedServers, baseConfig } = await loadMergedMcpServers(
+		const { servers, sharedServers, projectServers, baseConfig } = await loadMergedMcpServers(
 			options.agentDir,
 			options.projectDir,
 			options.homeDir !== undefined ? { homeDir: options.homeDir } : undefined,
@@ -460,6 +459,9 @@ export async function writeRuntimeFiles(
 
 		for (const sharedName of sharedServers) {
 			if (!allowedSet.has(sharedName)) {
+				// Project-level servers are not the profile's to narrow (the same
+				// boundary as project skills and extensions).
+				if (projectServers.has(sharedName)) continue;
 				filteredServers[sharedName] = { disabled: true };
 			}
 		}
@@ -494,9 +496,6 @@ export async function syncAgentSymlinks(agentDir: string, runtimeDir: string): P
 	if (!existsSync(agentDir)) return;
 	if (path.resolve(agentDir) === path.resolve(runtimeDir)) return;
 
-	// Ensure the real sessions directory exists so it is always mirrored
-	await mkdir(path.join(agentDir, "sessions"), { recursive: true });
-
 	// 1. Clean up dangling or obsolete symlinks in runtimeDir
 	try {
 		const runtimeEntries = await readdir(runtimeDir);
@@ -517,7 +516,13 @@ export async function syncAgentSymlinks(agentDir: string, runtimeDir: string): P
 		}
 	} catch {}
 
-	// 2. Mirror files and directories from agentDir to runtimeDir
+	// 2. Seed the state paths this process's Pi will create at runtime, so their
+	// writes land in the real agent dir instead of an instance-local copy
+	// (ADR-0010). Runs after the cleanup above, which would otherwise remove the
+	// deliberately dangling file links.
+	await seedRuntimeState(agentDir, runtimeDir);
+
+	// 3. Mirror files and directories from agentDir to runtimeDir
 	try {
 		const entries = await readdir(agentDir);
 		for (const name of entries) {
@@ -547,13 +552,45 @@ export async function syncAgentSymlinks(agentDir: string, runtimeDir: string): P
 	} catch {}
 }
 
+/** Ensures the runtime state paths exist (or are linked) in the real agent dir
+ *  and the instance. Best-effort: a failure here leaves the path unseeded, and
+ *  the sweep's unrecognized-entry warning names it later. */
+async function seedRuntimeState(agentDir: string, runtimeDir: string): Promise<void> {
+	for (const name of SEEDED_STATE_DIRS) {
+		try {
+			await mkdir(path.join(agentDir, name), { recursive: true });
+		} catch {
+			// Best-effort: the mirror then simply links nothing for this name.
+		}
+	}
+
+	for (const name of SEEDED_STATE_FILES) {
+		const linkPath = path.join(runtimeDir, name);
+		// A real file here belongs to an earlier run of a different layout, and a
+		// link may already point somewhere else: leave both alone rather than
+		// replacing state pi-profile cannot attribute.
+		if (await existsLexical(linkPath)) continue;
+		try {
+			await symlink(path.join(agentDir, name), linkPath);
+		} catch {
+			// Best-effort: Pi then creates the file inside the instance, and the
+			// sweep keeps that directory instead of deleting it silently.
+		}
+	}
+}
+
 export async function generateRuntimeDir(
 	plan: ActivationPlan,
 	options: GenerateOptions,
 ): Promise<GeneratedRuntime> {
 	const { agentDir } = options;
-	const runtimeDir = path.join(getInstancesRootDir(), plan.profile, "agent");
-	await mkdir(runtimeDir, { recursive: true });
+	const runtimeRoot = getInstancesRootDir();
+	await mkdir(runtimeRoot, { recursive: true });
+	// One instance per launch, never reused: PI_CODING_AGENT_DIR is frozen for
+	// the life of the spawned process, so a stable path cannot follow an
+	// in-session switch, and a shared path would make concurrent launches (and
+	// their switches) rewrite each other's files (ADR-0010).
+	const runtimeDir = await mkdtemp(path.join(runtimeRoot, "launch-"));
 
 	await writeRuntimeFiles(runtimeDir, plan, options);
 

package/src/skill-registry.ts

@@ -44,9 +44,9 @@ export interface DiscoverSkillsOptions {
 }
 
 export async function discoverSkills(options: DiscoverSkillsOptions): Promise<SkillEntry[]> {
-	// Project trust comes from the caller's trust check; generated settings
-	// carry defaultProjectTrust: "never", so discovery is the only place
-	// project resources can enter a plan.
+	// Project trust comes from the caller's trust check: discovery is the only
+	// place project resources enter a plan's reference vocabulary (their
+	// visibility in the session is Pi's, not the plan's).
 	const settingsManager = SettingsManager.create(options.cwd, options.agentDir, {
 		projectTrusted: options.projectTrusted ?? false,
 	});
@@ -73,10 +73,10 @@ export async function discoverSkills(options: DiscoverSkillsOptions): Promise<Sk
 		else process.env.PI_OFFLINE = savedOffline;
 	}
 	return loader.getSkills().skills.flatMap((skill) => {
-		// Project-scoped package skills are excluded: their packages install
-		// under the project's .pi/npm, which generated global-scope settings
-		// cannot reference. Project .pi/skills and ancestor .agents/skills are
-		// unaffected. (Limitation documented in ticket 03's comments.)
+		// Project-scoped package skills stay out of the reference vocabulary:
+		// their packages live under the project's .pi/npm and Pi discovers their
+		// skills natively, so a profile reference would add nothing. Project
+		// .pi/skills and ancestor .agents/skills are referenceable.
 		if (skill.sourceInfo.origin === "package" && skill.sourceInfo.scope === "project") {
 			return [];
 		}

package/src/switching/apply-plan.ts

@@ -48,7 +48,7 @@ export interface LaunchPlanFile {
 		skills: Array<{ name: string; filePath: string }>;
 		extensions: Array<{ id: string; entry: string }>;
 	};
-	/** Glob references that matched nothing at resolution (ADR-0006). */
+	/** Glob references that matched nothing at resolution (ADR-0009). */
 	unmatched?: string[];
 	previousResolved?: {
 		skills: string[];

package/src/switching/status.ts

@@ -36,7 +36,7 @@ export interface StatusReport {
 	mcp: { enabled: string[]; disabled: string[]; missing: string[] };
 	/** Glob delta versus the previous activation (prefixed names). */
 	delta?: { added: string[]; removed: string[] };
-	/** Glob references that matched nothing at resolution (ADR-0006). */
+	/** Glob references that matched nothing at resolution (ADR-0009). */
 	unmatched?: string[];
 	conflicts: StatusConflict[];
 }

package/src/switching/switch-profile.ts

@@ -204,7 +204,6 @@ export async function switchProfile(
 		agentDir: deps.realAgentDir,
 		projectDir: resolved.projectDir,
 		discovery: resolved.discovery,
-		projectSettings: resolved.projectSettings,
 		planExtras: {
 			...(isSwitch && current.profile !== undefined ? { switchedFrom: current.profile } : {}),
 			// `/profile use` persists; `/profile reload` keeps the current