refactor(coding-agent): drop project user config scope

packages/coding-agent/README.md

@@ -192,7 +192,7 @@ Type `/` in the editor to trigger commands. [Extensions](#extensions) can regist
 | `/export [file]` | Export session to HTML file |
 | `/share` | Upload as private GitHub gist with shareable HTML link |
 | `/reload` | Reload keybindings, extensions, skills, prompts, and context files (themes hot-reload automatically) |
-| `/trust [yes|no|reset]` | Configure whether `.pi` and `.pi.user` are trusted for this working directory |
+| `/trust [yes|no|reset]` | Configure whether `.pi` is trusted for this working directory |
 | `/hotkeys` | Show all keyboard shortcuts |
 | `/changelog` | Display version history |
 | `/quit` | Quit pi |
@@ -285,13 +285,12 @@ Use `/settings` to modify common options, or edit JSON files directly:
 |----------|-------|
 | `~/.pi/agent/settings.json` | Global (all projects) |
 | `.pi/settings.json` | Project (overrides global) |
-| `.pi.user/settings.json` | Project-local user overrides (ignored by Git when Pi creates it) |
 
 See [docs/settings.md](docs/settings.md) for all options.
 
 ### Project Trust
 
-Interactive startup asks before loading `.pi` or `.pi.user` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
+Interactive startup asks before loading `.pi` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
 
 ### Telemetry and update checks
 
@@ -317,7 +316,7 @@ Disable context file loading with `--no-context-files` (or `-nc`).
 
 ### System Prompt
 
-Replace the default system prompt with `.pi.user/SYSTEM.md` (project-local user), `.pi/SYSTEM.md` (project), or `~/.pi/agent/SYSTEM.md` (global). Append without replacing via `APPEND_SYSTEM.md` in the same locations.
+Replace the default system prompt with `.pi/SYSTEM.md` (project) or `~/.pi/agent/SYSTEM.md` (global). Append without replacing via `APPEND_SYSTEM.md`.
 
 ---
 
@@ -333,7 +332,7 @@ Review this code for bugs, security issues, and performance problems.
 Focus on: {{focus}}
 ```
 
-Place in `~/.pi/agent/prompts/`, `.pi/prompts/`, `.pi.user/prompts/`, or a [pi package](#pi-packages) to share with others. See [docs/prompt-templates.md](docs/prompt-templates.md).
+Place in `~/.pi/agent/prompts/`, `.pi/prompts/`, or a [pi package](#pi-packages) to share with others. See [docs/prompt-templates.md](docs/prompt-templates.md).
 
 ### Skills
 
@@ -349,7 +348,7 @@ Use this skill when the user asks about X.
 2. Then that
 ```
 
-Place in `~/.pi/agent/skills/`, `~/.agents/skills/`, `.pi/skills/`, `.pi.user/skills/`, or `.agents/skills/` (from `cwd` up through parent directories) or a [pi package](#pi-packages) to share with others. See [docs/skills.md](docs/skills.md).
+Place in `~/.pi/agent/skills/`, `~/.agents/skills/`, `.pi/skills/`, or `.agents/skills/` (from `cwd` up through parent directories) or a [pi package](#pi-packages) to share with others. See [docs/skills.md](docs/skills.md).
 
 ### Extensions
 
@@ -381,13 +380,13 @@ The default export can also be `async`. pi waits for async extension factories b
 - Games while waiting (yes, Doom runs)
 - ...anything you can dream up
 
-Place in `~/.pi/agent/extensions/`, `.pi/extensions/`, `.pi.user/extensions/`, or a [pi package](#pi-packages) to share with others. See [docs/extensions.md](docs/extensions.md) and [examples/extensions/](examples/extensions/).
+Place in `~/.pi/agent/extensions/`, `.pi/extensions/`, or a [pi package](#pi-packages) to share with others. See [docs/extensions.md](docs/extensions.md) and [examples/extensions/](examples/extensions/).
 
 ### Themes
 
 Built-in: `dark`, `light`. Themes hot-reload: modify the active theme file and pi immediately applies changes.
 
-Place in `~/.pi/agent/themes/`, `.pi/themes/`, `.pi.user/themes/`, or a [pi package](#pi-packages) to share with others. See [docs/themes.md](docs/themes.md).
+Place in `~/.pi/agent/themes/`, `.pi/themes/`, or a [pi package](#pi-packages) to share with others. See [docs/themes.md](docs/themes.md).
 
 ### Pi Packages
 
@@ -417,7 +416,7 @@ pi update npm:@foo/pi-tools             # update one package
 pi config                               # enable/disable extensions, skills, prompts, themes
 ```
 
-Packages install to `~/.pi/agent/git/` (git) or `~/.pi/agent/npm/` (npm). Use `-l` for project-local installs (`.pi/git/`, `.pi/npm/`), or `-l -u` for ignored project-local user installs (`.pi.user/git/`, `.pi.user/npm/`). Git `@ref` values are pinned tags or commits; pinned packages are skipped by `pi update`, so use `pi install git:host/user/repo@new-ref` to move an existing package to a new ref. Git packages install dependencies with `npm install --omit=dev` by default, so runtime deps must be listed under `dependencies`; when `npmCommand` is configured, git packages use plain `install` for compatibility with wrappers. If you use a Node version manager and want package installs to reuse a stable npm context, set `npmCommand` in `settings.json`, for example `["mise", "exec", "node@20", "--", "npm"]`.
+Packages install to `~/.pi/agent/git/` (git) or `~/.pi/agent/npm/` (npm). Use `-l` for project-local installs (`.pi/git/`, `.pi/npm/`). Git `@ref` values are pinned tags or commits; pinned packages are skipped by `pi update`, so use `pi install git:host/user/repo@new-ref` to move an existing package to a new ref. Git packages install dependencies with `npm install --omit=dev` by default, so runtime deps must be listed under `dependencies`; when `npmCommand` is configured, git packages use plain `install` for compatibility with wrappers. If you use a Node version manager and want package installs to reuse a stable npm context, set `npmCommand` in `settings.json`, for example `["mise", "exec", "node@20", "--", "npm"]`.
 
 Create a package by adding a `pi` key to `package.json`:
 
@@ -505,9 +504,9 @@ pi [options] [@files...] [messages...]
 ### Package Commands
 
 ```bash
-pi install <source> [-l] [-u] # Install package, -l for project-local, -u for .pi.user with -l
-pi remove <source> [-l] [-u]  # Remove package
-pi uninstall <source> [-l] [-u] # Alias for remove
+pi install <source> [-l]     # Install package, -l for project-local
+pi remove <source> [-l]      # Remove package
+pi uninstall <source> [-l]   # Alias for remove
 pi update [source|self|pi]   # Update pi and packages (skips pinned packages)
 pi update --extensions       # Update packages only
 pi update --self             # Update pi only
@@ -590,7 +589,7 @@ Combine `--no-*` with explicit flags to load exactly what you need, ignoring set
 | `--system-prompt <text>` | Replace default prompt (context files and skills still appended) |
 | `--append-system-prompt <text>` | Append to system prompt |
 | `--verbose` | Force verbose startup |
-| `-f`, `--force` | Force loading project `.pi` and `.pi.user` config regardless of trust |
+| `-f`, `--force` | Force loading project `.pi` config regardless of trust |
 | `-h`, `--help` | Show help |
 | `-v`, `--version` | Show version |
 

packages/coding-agent/docs/extensions.md

@@ -4,7 +4,7 @@
 
 Extensions are TypeScript modules that extend pi's behavior. They can subscribe to lifecycle events, register custom tools callable by the LLM, add commands, and more.
 
-> **Placement for /reload:** Put extensions in `~/.pi/agent/extensions/` (global), `.pi/extensions/` (project-local), or `.pi.user/extensions/` (project-local user) for auto-discovery. Use `pi -e ./path.ts` only for quick tests. Extensions in auto-discovered locations can be hot-reloaded with `/reload`.
+> **Placement for /reload:** Put extensions in `~/.pi/agent/extensions/` (global) or `.pi/extensions/` (project-local) for auto-discovery. Use `pi -e ./path.ts` only for quick tests. Extensions in auto-discovered locations can be hot-reloaded with `/reload`.
 
 **Key capabilities:**
 - **Custom tools** - Register tools the LLM can call via `pi.registerTool()`
@@ -117,8 +117,6 @@ Extensions are auto-discovered from:
 | `~/.pi/agent/extensions/*/index.ts` | Global (subdirectory) |
 | `.pi/extensions/*.ts` | Project-local |
 | `.pi/extensions/*/index.ts` | Project-local (subdirectory) |
-| `.pi.user/extensions/*.ts` | Project-local user |
-| `.pi.user/extensions/*/index.ts` | Project-local user (subdirectory) |
 
 Additional paths via `settings.json`:
 

packages/coding-agent/docs/packages.md

@@ -38,7 +38,7 @@ pi update --extension npm:@foo/bar
 
 These commands manage pi packages, not the pi CLI installation. To uninstall pi itself, see [Quickstart](quickstart.md#uninstall).
 
-By default, `install` and `remove` write to user settings (`~/.pi/agent/settings.json`). Use `-l` to write to project settings (`.pi/settings.json`) instead. Use `-l -u` to write to ignored project-local user settings (`.pi.user/settings.json`). Project settings can be shared with your team, and pi installs any missing packages automatically on startup.
+By default, `install` and `remove` write to user settings (`~/.pi/agent/settings.json`). Use `-l` to write to project settings (`.pi/settings.json`) instead. Project settings can be shared with your team, and pi installs any missing packages automatically on startup.
 
 To try a package without installing it, use `--extension` or `-e`. This installs to a temporary directory for the current run only:
 
@@ -60,7 +60,7 @@ npm:pkg
 
 - Versioned specs are pinned and skipped by package updates (`pi update`, `pi update --extensions`).
 - User installs go under `~/.pi/agent/npm/`.
-- Project installs go under `.pi/npm/`; project-local user installs go under `.pi.user/npm/`.
+- Project installs go under `.pi/npm/`.
 - Set `npmCommand` in `settings.json` to pin npm package lookup and install operations to a specific wrapper command such as `mise` or `asdf`.
 
 Example:
@@ -87,7 +87,7 @@ ssh://git@github.com/user/repo@v1
 - For non-interactive runs (for example CI), you can set `GIT_TERMINAL_PROMPT=0` to disable credential prompts and set `GIT_SSH_COMMAND` (for example `ssh -o BatchMode=yes -o ConnectTimeout=5`) to fail fast.
 - Refs are pinned tags or commits. `pi update` and `pi update --extensions` do not move them to newer refs, but they do reconcile an existing clone to the configured ref.
 - Use `pi install git:host/user/repo@new-ref` to update settings and move an existing package to a new pinned ref.
-- Cloned to `~/.pi/agent/git/<host>/<path>` (global), `.pi/git/<host>/<path>` (project), or `.pi.user/git/<host>/<path>` (project-local user).
+- Cloned to `~/.pi/agent/git/<host>/<path>` (global) or `.pi/git/<host>/<path>` (project).
 - When reconciliation changes the checkout, pi resets and cleans the clone, then runs `npm install` if `package.json` exists.
 
 **SSH examples:**
@@ -219,7 +219,7 @@ Use `pi config` to enable or disable extensions, skills, prompt templates, and t
 
 ## Scope and Deduplication
 
-Packages can appear in global, project, and project-local user settings. If the same package appears in more than one scope, `.pi.user` wins over `.pi`, and project scopes win over global. Identity is determined by:
+Packages can appear in both global and project settings. If the same package appears in both, the project entry wins. Identity is determined by:
 
 - npm: package name
 - git: repository URL without ref

packages/coding-agent/docs/prompt-templates.md

@@ -9,7 +9,7 @@ Prompt templates are Markdown snippets that expand into full prompts. Type `/nam
 Pi loads prompt templates from:
 
 - Global: `~/.pi/agent/prompts/*.md`
-- Project: `.pi/prompts/*.md`, `.pi.user/prompts/*.md`
+- Project: `.pi/prompts/*.md`
 - Packages: `prompts/` directories or `pi.prompts` entries in `package.json`
 - Settings: `prompts` array with files or directories
 - CLI: `--prompt-template <path>` (repeatable)

packages/coding-agent/docs/settings.md

@@ -1,18 +1,17 @@
 # Settings
 
-Pi uses JSON settings files with project settings overriding global settings and `.pi.user` overriding shared project settings.
+Pi uses JSON settings files with project settings overriding global settings.
 
 | Location | Scope |
 |----------|-------|
 | `~/.pi/agent/settings.json` | Global (all projects) |
 | `.pi/settings.json` | Project (current directory) |
-| `.pi.user/settings.json` | Project-local user overrides (ignored by Git when Pi creates it) |
 
 Edit directly or use `/settings` for common options.
 
 ## Project Trust
 
-Interactive startup asks before loading `.pi` or `.pi.user` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
+Interactive startup asks before loading `.pi` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
 
 ## All Settings
 
@@ -198,7 +197,7 @@ When multiple sources specify a session directory, precedence is `--session-dir`
 
 These settings define where to load extensions, skills, prompts, and themes from.
 
-Paths in `~/.pi/agent/settings.json` resolve relative to `~/.pi/agent`. Paths in `.pi/settings.json` resolve relative to `.pi`; paths in `.pi.user/settings.json` resolve relative to `.pi.user`. Absolute paths and `~` are supported.
+Paths in `~/.pi/agent/settings.json` resolve relative to `~/.pi/agent`. Paths in `.pi/settings.json` resolve relative to `.pi`. Absolute paths and `~` are supported.
 
 | Setting | Type | Default | Description |
 |---------|------|---------|-------------|
@@ -264,7 +263,7 @@ See [packages.md](packages.md) for package management details.
 
 ## Project Overrides
 
-Project settings (`.pi/settings.json`) override global settings. Project-local user settings (`.pi.user/settings.json`) override both. Nested objects are merged:
+Project settings (`.pi/settings.json`) override global settings. Nested objects are merged:
 
 ```json
 // ~/.pi/agent/settings.json (global)
@@ -278,14 +277,9 @@ Project settings (`.pi/settings.json`) override global settings. Project-local u
   "compaction": { "reserveTokens": 8192 }
 }
 
-// .pi.user/settings.json (project-local user)
-{
-  "theme": "light"
-}
-
 // Result
 {
-  "theme": "light",
+  "theme": "dark",
   "compaction": { "enabled": true, "reserveTokens": 8192 }
 }
 ```

packages/coding-agent/docs/skills.md

@@ -28,14 +28,13 @@ Pi loads skills from:
   - `~/.agents/skills/`
 - Project:
   - `.pi/skills/`
-  - `.pi.user/skills/`
   - `.agents/skills/` in `cwd` and ancestor directories (up to git repo root, or filesystem root when not in a repo)
 - Packages: `skills/` directories or `pi.skills` entries in `package.json`
 - Settings: `skills` array with files or directories
 - CLI: `--skill <path>` (repeatable, additive even with `--no-skills`)
 
 Discovery rules:
-- In `~/.pi/agent/skills/`, `.pi/skills/`, and `.pi.user/skills/`, direct root `.md` files are discovered as individual skills
+- In `~/.pi/agent/skills/` and `.pi/skills/`, direct root `.md` files are discovered as individual skills
 - In all skill locations, directories containing `SKILL.md` are discovered recursively
 - In `~/.agents/skills/` and project `.agents/skills/`, root `.md` files are ignored
 

packages/coding-agent/docs/themes.md

@@ -20,7 +20,7 @@ Pi loads themes from:
 
 - Built-in: `dark`, `light`
 - Global: `~/.pi/agent/themes/*.json`
-- Project: `.pi/themes/*.json`, `.pi.user/themes/*.json`
+- Project: `.pi/themes/*.json`
 - Packages: `themes/` directories or `pi.themes` entries in `package.json`
 - Settings: `themes` array with files or directories
 - CLI: `--theme <path>` (repeatable)

packages/coding-agent/docs/usage.md

@@ -51,7 +51,7 @@ Type `/` in the editor to open command completion. Extensions can register custo
 | `/export [file]` | Export session to HTML |
 | `/share` | Upload as private GitHub gist with shareable HTML link |
 | `/reload` | Reload keybindings, extensions, skills, prompts, and context files |
-| `/trust [yes|no|reset]` | Configure whether `.pi` and `.pi.user` are trusted for this working directory |
+| `/trust [yes|no|reset]` | Configure whether `.pi` is trusted for this working directory |
 | `/hotkeys` | Show all keyboard shortcuts |
 | `/changelog` | Display version history |
 | `/quit` | Quit pi |
@@ -106,7 +106,6 @@ Use context files for project conventions, commands, safety rules, and preferenc
 
 Replace the default system prompt with:
 
-- `.pi.user/SYSTEM.md` for project-local user overrides
 - `.pi/SYSTEM.md` for a project
 - `~/.pi/agent/SYSTEM.md` globally
 
@@ -114,7 +113,7 @@ Append to the default prompt without replacing it with `APPEND_SYSTEM.md` in tho
 
 ### Project Trust
 
-Interactive startup asks before loading `.pi` or `.pi.user` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
+Interactive startup asks before loading `.pi` in a working directory whose trust has not been set. Decisions are stored in `~/.pi/agent/trust.json` by CWD: `true` loads project config, `false` skips it, and missing/null asks again. Use `/trust yes`, `/trust no`, `/trust reset`, or `/trust` to update the current CWD. Use `--force`/`-f` to load project config for one run regardless of trust.
 
 ## Exporting and Sharing Sessions
 
@@ -133,9 +132,9 @@ pi [options] [@files...] [messages...]
 ### Package Commands
 
 ```bash
-pi install <source> [-l] [-u] # Install package, -l for project-local, -u for .pi.user with -l
-pi remove <source> [-l] [-u]  # Remove package
-pi uninstall <source> [-l] [-u] # Alias for remove
+pi install <source> [-l]     # Install package, -l for project-local
+pi remove <source> [-l]      # Remove package
+pi uninstall <source> [-l]   # Alias for remove
 pi update [source|self|pi]   # Update pi and packages; reconcile pinned git refs
 pi update --extensions       # Update packages only; reconcile pinned git refs
 pi update --self             # Update pi only
@@ -225,7 +224,7 @@ pi --no-extensions -e ./my-extension.ts
 | `--system-prompt <text>` | Replace default prompt; context files and skills are still appended |
 | `--append-system-prompt <text>` | Append to system prompt |
 | `--verbose` | Force verbose startup |
-| `-f`, `--force` | Force loading project `.pi` and `.pi.user` config regardless of trust |
+| `-f`, `--force` | Force loading project `.pi` config regardless of trust |
 | `-h`, `--help` | Show help |
 | `-v`, `--version` | Show version |
 

packages/coding-agent/src/cli/args.ts

@@ -224,9 +224,9 @@ ${chalk.bold("Usage:")}
   ${APP_NAME} [options] [@files...] [messages...]
 
 ${chalk.bold("Commands:")}
-  ${APP_NAME} install <source> [-l] [-u]  Install extension source and add to settings
-  ${APP_NAME} remove <source> [-l] [-u]   Remove extension source from settings
-  ${APP_NAME} uninstall <source> [-l] [-u] Alias for remove
+  ${APP_NAME} install <source> [-l]     Install extension source and add to settings
+  ${APP_NAME} remove <source> [-l]      Remove extension source from settings
+  ${APP_NAME} uninstall <source> [-l]   Alias for remove
   ${APP_NAME} update [source|self|pi]   Update pi and installed extensions
   ${APP_NAME} list [--force]            List installed extensions from settings
   ${APP_NAME} config                    Open TUI to enable/disable package resources
@@ -269,7 +269,7 @@ ${chalk.bold("Options:")}
   --export <file>                Export session file to HTML and exit
   --list-models [search]         List available models (with optional fuzzy search)
   --verbose                      Force verbose startup (overrides quietStartup setting)
-  --force, -f                    Force loading project .pi and .pi.user config
+  --force, -f                    Force loading project .pi config
   --offline                      Disable startup network operations (same as PI_OFFLINE=1)
   --help, -h                     Show this help
   --version, -v                  Show version number

packages/coding-agent/src/config.ts

@@ -465,7 +465,6 @@ export const PACKAGE_NAME: string = pkg.name || "@earendil-works/pi-coding-agent
 export const APP_NAME: string = piConfigName || "pi";
 export const APP_TITLE: string = piConfigName ? APP_NAME : "π";
 export const CONFIG_DIR_NAME: string = pkg.piConfig?.configDir || ".pi";
-export const PROJECT_USER_CONFIG_DIR_NAME = `${CONFIG_DIR_NAME}.user`;
 export const VERSION: string = pkg.version || "0.0.0";
 
 // e.g., PI_CODING_AGENT_DIR or TAU_CODING_AGENT_DIR

packages/coding-agent/src/core/package-manager.ts

@@ -27,12 +27,11 @@ import type { Readable } from "node:stream";
 import { globSync } from "glob";
 import ignore from "ignore";
 import { minimatch } from "minimatch";
-import { CONFIG_DIR_NAME, PROJECT_USER_CONFIG_DIR_NAME } from "../config.ts";
+import { CONFIG_DIR_NAME } from "../config.ts";
 import { spawnProcess, spawnProcessSync } from "../utils/child-process.ts";
 import { type GitSource, parseGitUrl } from "../utils/git.ts";
 import { canonicalizePath, isLocalPath, markPathIgnoredByCloudSync, resolvePath } from "../utils/paths.ts";
 import { isStdoutTakenOver } from "./output-guard.ts";
-import { ensureIgnoredProjectUserConfigDir } from "./project-user-config.ts";
 import type { PackageSource, SettingsManager } from "./settings-manager.ts";
 
 const NETWORK_TIMEOUT_MS = 10000;
@@ -45,12 +44,9 @@ function isOfflineModeEnabled(): boolean {
 	return value === "1" || value.toLowerCase() === "true" || value.toLowerCase() === "yes";
 }
 
-export type SettingsSourceScope = "user" | "project" | "projectUser";
-export type ResourceMetadataScope = SettingsSourceScope | "temporary";
-
 export interface PathMetadata {
 	source: string;
-	scope: ResourceMetadataScope;
+	scope: SourceScope;
 	origin: "package" | "top-level";
 	baseDir?: string;
 }
@@ -83,32 +79,32 @@ export interface PackageUpdate {
 	source: string;
 	displayName: string;
 	type: "npm" | "git";
-	scope: InstalledSourceScope;
+	scope: Exclude<SourceScope, "temporary">;
 }
 
 export interface ConfiguredPackage {
 	source: string;
-	scope: InstalledSourceScope;
+	scope: "user" | "project";
 	filtered: boolean;
 	installedPath?: string;
 }
 
 export interface PackageManager {
 	resolve(onMissing?: (source: string) => Promise<MissingSourceAction>): Promise<ResolvedPaths>;
-	install(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void>;
-	installAndPersist(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void>;
-	remove(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void>;
-	removeAndPersist(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<boolean>;
+	install(source: string, options?: { local?: boolean }): Promise<void>;
+	installAndPersist(source: string, options?: { local?: boolean }): Promise<void>;
+	remove(source: string, options?: { local?: boolean }): Promise<void>;
+	removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean>;
 	update(source?: string): Promise<void>;
 	listConfiguredPackages(): ConfiguredPackage[];
 	resolveExtensionSources(
 		sources: string[],
 		options?: { local?: boolean; temporary?: boolean },
 	): Promise<ResolvedPaths>;
-	addSourceToSettings(source: string, options?: { local?: boolean; localUser?: boolean }): boolean;
-	removeSourceFromSettings(source: string, options?: { local?: boolean; localUser?: boolean }): boolean;
+	addSourceToSettings(source: string, options?: { local?: boolean }): boolean;
+	removeSourceFromSettings(source: string, options?: { local?: boolean }): boolean;
 	setProgressCallback(callback: ProgressCallback | undefined): void;
-	getInstalledPath(source: string, scope: InstalledSourceScope): string | undefined;
+	getInstalledPath(source: string, scope: "user" | "project"): string | undefined;
 }
 
 interface PackageManagerOptions {
@@ -117,7 +113,7 @@ interface PackageManagerOptions {
 	settingsManager: SettingsManager;
 }
 
-type SourceScope = SettingsSourceScope | "temporary";
+type SourceScope = "user" | "project" | "temporary";
 
 type NpmSource = {
 	type: "npm";
@@ -133,7 +129,7 @@ type LocalSource = {
 
 type ParsedSource = NpmSource | GitSource | LocalSource;
 
-export type InstalledSourceScope = SettingsSourceScope;
+type InstalledSourceScope = Exclude<SourceScope, "temporary">;
 
 interface ConfiguredUpdateSource {
 	source: string;
@@ -168,17 +164,15 @@ interface ResourceAccumulator {
  * name-collision resolution ("first wins") produces the correct outcome.
  *
  * Precedence (highest to lowest):
- *   0  .pi.user + settings entry
- *   1  .pi.user + auto-discovered
- *   2  .pi + settings entry
- *   3  .pi + auto-discovered
- *   4  user + settings entry
- *   5  user + auto-discovered
- *   6  package resource
+ *   0  project + settings entry (source: "local", scope: "project")
+ *   1  project + auto-discovered (source: "auto", scope: "project")
+ *   2  user + settings entry (source: "local", scope: "user")
+ *   3  user + auto-discovered (source: "auto", scope: "user")
+ *   4  package resource (origin: "package")
  */
 function resourcePrecedenceRank(m: PathMetadata): number {
-	if (m.origin === "package") return 6;
-	const scopeBase = m.scope === "projectUser" ? 0 : m.scope === "project" ? 2 : m.scope === "user" ? 4 : 6;
+	if (m.origin === "package") return 4;
+	const scopeBase = m.scope === "project" ? 0 : 2;
 	return scopeBase + (m.source === "local" ? 0 : 1);
 }
 
@@ -778,36 +772,10 @@ export class DefaultPackageManager implements PackageManager {
 		this.progressCallback = callback;
 	}
 
-	private getScopeForOptions(options?: { local?: boolean; localUser?: boolean }): InstalledSourceScope {
-		if (options?.localUser) {
-			return "projectUser";
-		}
-		return options?.local ? "project" : "user";
-	}
-
-	private getSettingsForScope(scope: InstalledSourceScope) {
-		if (scope === "projectUser") {
-			return this.settingsManager.getProjectUserSettings();
-		}
-		if (scope === "project") {
-			return this.settingsManager.getProjectSettings();
-		}
-		return this.settingsManager.getGlobalSettings();
-	}
-
-	private setPackagesForScope(scope: InstalledSourceScope, packages: PackageSource[]): void {
-		if (scope === "projectUser") {
-			this.settingsManager.setProjectUserPackages(packages);
-		} else if (scope === "project") {
-			this.settingsManager.setProjectPackages(packages);
-		} else {
-			this.settingsManager.setPackages(packages);
-		}
-	}
-
-	addSourceToSettings(source: string, options?: { local?: boolean; localUser?: boolean }): boolean {
-		const scope = this.getScopeForOptions(options);
-		const currentSettings = this.getSettingsForScope(scope);
+	addSourceToSettings(source: string, options?: { local?: boolean }): boolean {
+		const scope: SourceScope = options?.local ? "project" : "user";
+		const currentSettings =
+			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
 		const currentPackages = currentSettings.packages ?? [];
 		const normalizedSource = this.normalizePackageSourceForSettings(source, scope);
 		const matchIndex = currentPackages.findIndex((existing) => this.packageSourcesMatch(existing, source, scope));
@@ -819,28 +787,41 @@ export class DefaultPackageManager implements PackageManager {
 			const nextPackages = [...currentPackages];
 			nextPackages[matchIndex] =
 				typeof existing === "string" ? normalizedSource : { ...existing, source: normalizedSource };
-			this.setPackagesForScope(scope, nextPackages);
+			if (scope === "project") {
+				this.settingsManager.setProjectPackages(nextPackages);
+			} else {
+				this.settingsManager.setPackages(nextPackages);
+			}
 			return true;
 		}
 		const nextPackages = [...currentPackages, normalizedSource];
-		this.setPackagesForScope(scope, nextPackages);
+		if (scope === "project") {
+			this.settingsManager.setProjectPackages(nextPackages);
+		} else {
+			this.settingsManager.setPackages(nextPackages);
+		}
 		return true;
 	}
 
-	removeSourceFromSettings(source: string, options?: { local?: boolean; localUser?: boolean }): boolean {
-		const scope = this.getScopeForOptions(options);
-		const currentSettings = this.getSettingsForScope(scope);
+	removeSourceFromSettings(source: string, options?: { local?: boolean }): boolean {
+		const scope: SourceScope = options?.local ? "project" : "user";
+		const currentSettings =
+			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
 		const currentPackages = currentSettings.packages ?? [];
 		const nextPackages = currentPackages.filter((existing) => !this.packageSourcesMatch(existing, source, scope));
 		const changed = nextPackages.length !== currentPackages.length;
 		if (!changed) {
 			return false;
 		}
-		this.setPackagesForScope(scope, nextPackages);
+		if (scope === "project") {
+			this.settingsManager.setProjectPackages(nextPackages);
+		} else {
+			this.settingsManager.setPackages(nextPackages);
+		}
 		return true;
 	}
 
-	getInstalledPath(source: string, scope: InstalledSourceScope): string | undefined {
+	getInstalledPath(source: string, scope: "user" | "project"): string | undefined {
 		const parsed = this.parseSource(source);
 		if (parsed.type === "npm") {
 			const path = this.getNpmInstallPath(parsed, scope);
@@ -882,42 +863,39 @@ export class DefaultPackageManager implements PackageManager {
 	async resolve(onMissing?: (source: string) => Promise<MissingSourceAction>): Promise<ResolvedPaths> {
 		const accumulator = this.createAccumulator();
 		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectLayers = this.settingsManager.getProjectSettingsLayers();
+		const projectSettings = this.settingsManager.getProjectSettings();
 
-		// Collect all packages with scope (project-local user first so it wins collisions)
+		// Collect all packages with scope (project first so cwd resources win collisions)
 		const allPackages: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
-		for (const layer of projectLayers) {
-			for (const pkg of layer.settings.packages ?? []) {
-				allPackages.push({ pkg, scope: layer.scope });
-			}
+		for (const pkg of projectSettings.packages ?? []) {
+			allPackages.push({ pkg, scope: "project" });
 		}
 		for (const pkg of globalSettings.packages ?? []) {
 			allPackages.push({ pkg, scope: "user" });
 		}
 
-		// Dedupe: earlier scopes win for the same package identity.
+		// Dedupe: project scope wins over global for same package identity
 		const packageSources = this.dedupePackages(allPackages);
 		await this.resolvePackageSources(packageSources, accumulator, onMissing);
 
 		const globalBaseDir = this.agentDir;
+		const projectBaseDir = join(this.cwd, CONFIG_DIR_NAME);
 
 		for (const resourceType of RESOURCE_TYPES) {
 			const target = this.getTargetMap(accumulator, resourceType);
 			const globalEntries = (globalSettings[resourceType] ?? []) as string[];
-			for (const layer of projectLayers) {
-				const projectEntries = (layer.settings[resourceType] ?? []) as string[];
-				this.resolveLocalEntries(
-					projectEntries,
-					resourceType,
-					target,
-					{
-						source: "local",
-						scope: layer.scope,
-						origin: "top-level",
-					},
-					this.getBaseDirForScope(layer.scope),
-				);
-			}
+			const projectEntries = (projectSettings[resourceType] ?? []) as string[];
+			this.resolveLocalEntries(
+				projectEntries,
+				resourceType,
+				target,
+				{
+					source: "local",
+					scope: "project",
+					origin: "top-level",
+				},
+				projectBaseDir,
+			);
 			this.resolveLocalEntries(
 				globalEntries,
 				resourceType,
@@ -931,7 +909,7 @@ export class DefaultPackageManager implements PackageManager {
 			);
 		}
 
-		this.addAutoDiscoveredResources(accumulator, globalSettings, projectLayers, globalBaseDir);
+		this.addAutoDiscoveredResources(accumulator, globalSettings, projectSettings, globalBaseDir, projectBaseDir);
 
 		return this.toResolvedPaths(accumulator);
 	}
@@ -949,7 +927,7 @@ export class DefaultPackageManager implements PackageManager {
 
 	listConfiguredPackages(): ConfiguredPackage[] {
 		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectLayers = this.settingsManager.getProjectSettingsLayers();
+		const projectSettings = this.settingsManager.getProjectSettings();
 		const configuredPackages: ConfiguredPackage[] = [];
 
 		for (const pkg of globalSettings.packages ?? []) {
@@ -962,24 +940,22 @@ export class DefaultPackageManager implements PackageManager {
 			});
 		}
 
-		for (const layer of projectLayers) {
-			for (const pkg of layer.settings.packages ?? []) {
-				const source = typeof pkg === "string" ? pkg : pkg.source;
-				configuredPackages.push({
-					source,
-					scope: layer.scope,
-					filtered: typeof pkg === "object",
-					installedPath: this.getInstalledPath(source, layer.scope),
-				});
-			}
+		for (const pkg of projectSettings.packages ?? []) {
+			const source = typeof pkg === "string" ? pkg : pkg.source;
+			configuredPackages.push({
+				source,
+				scope: "project",
+				filtered: typeof pkg === "object",
+				installedPath: this.getInstalledPath(source, "project"),
+			});
 		}
 
 		return configuredPackages;
 	}
 
-	async install(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void> {
+	async install(source: string, options?: { local?: boolean }): Promise<void> {
 		const parsed = this.parseSource(source);
-		const scope: SourceScope = this.getScopeForOptions(options);
+		const scope: SourceScope = options?.local ? "project" : "user";
 		await this.withProgress("install", source, `Installing ${source}...`, async () => {
 			if (parsed.type === "npm") {
 				await this.installNpm(parsed, scope, false);
@@ -1000,14 +976,14 @@ export class DefaultPackageManager implements PackageManager {
 		});
 	}
 
-	async installAndPersist(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void> {
+	async installAndPersist(source: string, options?: { local?: boolean }): Promise<void> {
 		await this.install(source, options);
 		this.addSourceToSettings(source, options);
 	}
 
-	async remove(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<void> {
+	async remove(source: string, options?: { local?: boolean }): Promise<void> {
 		const parsed = this.parseSource(source);
-		const scope: SourceScope = this.getScopeForOptions(options);
+		const scope: SourceScope = options?.local ? "project" : "user";
 		await this.withProgress("remove", source, `Removing ${source}...`, async () => {
 			if (parsed.type === "npm") {
 				await this.uninstallNpm(parsed, scope);
@@ -1024,14 +1000,14 @@ export class DefaultPackageManager implements PackageManager {
 		});
 	}
 
-	async removeAndPersist(source: string, options?: { local?: boolean; localUser?: boolean }): Promise<boolean> {
+	async removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean> {
 		await this.remove(source, options);
 		return this.removeSourceFromSettings(source, options);
 	}
 
 	async update(source?: string): Promise<void> {
 		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectLayers = this.settingsManager.getProjectSettingsLayers();
+		const projectSettings = this.settingsManager.getProjectSettings();
 		const identity = source ? this.getPackageIdentity(source) : undefined;
 		let matched = false;
 		const updateSources: ConfiguredUpdateSource[] = [];
@@ -1042,20 +1018,18 @@ export class DefaultPackageManager implements PackageManager {
 			matched = true;
 			updateSources.push({ source: sourceStr, scope: "user" });
 		}
-		for (const layer of projectLayers) {
-			for (const pkg of layer.settings.packages ?? []) {
-				const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
-				if (identity && this.getPackageIdentity(sourceStr, layer.scope) !== identity) continue;
-				matched = true;
-				updateSources.push({ source: sourceStr, scope: layer.scope });
-			}
+		for (const pkg of projectSettings.packages ?? []) {
+			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
+			if (identity && this.getPackageIdentity(sourceStr, "project") !== identity) continue;
+			matched = true;
+			updateSources.push({ source: sourceStr, scope: "project" });
 		}
 
 		if (source && !matched) {
 			throw new Error(
 				this.buildNoMatchingPackageMessage(source, [
 					...(globalSettings.packages ?? []),
-					...projectLayers.flatMap((layer) => layer.settings.packages ?? []),
+					...(projectSettings.packages ?? []),
 				]),
 			);
 		}
@@ -1089,21 +1063,25 @@ export class DefaultPackageManager implements PackageManager {
 			shouldUpdate: await this.shouldUpdateNpmSource(entry.parsed, entry.scope),
 		}));
 		const npmCheckResults = await this.runWithConcurrency(npmCheckTasks, UPDATE_CHECK_CONCURRENCY);
-		const npmUpdatesByScope = new Map<InstalledSourceScope, NpmUpdateTarget[]>();
+		const userNpmUpdates: NpmUpdateTarget[] = [];
+		const projectNpmUpdates: NpmUpdateTarget[] = [];
 		for (const result of npmCheckResults) {
 			if (!result.shouldUpdate) {
 				continue;
 			}
-			const updates = npmUpdatesByScope.get(result.entry.scope) ?? [];
-			updates.push(result.entry);
-			npmUpdatesByScope.set(result.entry.scope, updates);
+			if (result.entry.scope === "user") {
+				userNpmUpdates.push(result.entry);
+			} else {
+				projectNpmUpdates.push(result.entry);
+			}
 		}
 
 		const tasks: Promise<void>[] = [];
-		for (const [scope, updates] of npmUpdatesByScope.entries()) {
-			if (updates.length > 0) {
-				tasks.push(this.updateNpmBatch(updates, scope));
-			}
+		if (userNpmUpdates.length > 0) {
+			tasks.push(this.updateNpmBatch(userNpmUpdates, "user"));
+		}
+		if (projectNpmUpdates.length > 0) {
+			tasks.push(this.updateNpmBatch(projectNpmUpdates, "project"));
 		}
 		if (gitCandidates.length > 0) {
 			const gitTasks = gitCandidates.map(
@@ -1160,12 +1138,10 @@ export class DefaultPackageManager implements PackageManager {
 		}
 
 		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectLayers = this.settingsManager.getProjectSettingsLayers();
+		const projectSettings = this.settingsManager.getProjectSettings();
 		const allPackages: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
-		for (const layer of projectLayers) {
-			for (const pkg of layer.settings.packages ?? []) {
-				allPackages.push({ pkg, scope: layer.scope });
-			}
+		for (const pkg of projectSettings.packages ?? []) {
+			allPackages.push({ pkg, scope: "project" });
 		}
 		for (const pkg of globalSettings.packages ?? []) {
 			allPackages.push({ pkg, scope: "user" });
@@ -1173,7 +1149,10 @@ export class DefaultPackageManager implements PackageManager {
 
 		const packageSources = this.dedupePackages(allPackages);
 		const checks = packageSources
-			.filter((entry): entry is { pkg: PackageSource; scope: InstalledSourceScope } => entry.scope !== "temporary")
+			.filter(
+				(entry): entry is { pkg: PackageSource; scope: Exclude<SourceScope, "temporary"> } =>
+					entry.scope !== "temporary",
+			)
 			.map((entry) => async (): Promise<PackageUpdate | undefined> => {
 				const source = typeof entry.pkg === "string" ? entry.pkg : entry.pkg.source;
 				const parsed = this.parseSource(source);
@@ -1227,11 +1206,7 @@ export class DefaultPackageManager implements PackageManager {
 			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
 			const filter = typeof pkg === "object" ? pkg : undefined;
 			const parsed = this.parseSource(sourceStr);
-			const metadata: PathMetadata = {
-				source: sourceStr,
-				scope,
-				origin: "package",
-			};
+			const metadata: PathMetadata = { source: sourceStr, scope, origin: "package" };
 
 			if (parsed.type === "local") {
 				const baseDir = this.getBaseDirForScope(scope);
@@ -1655,8 +1630,8 @@ export class DefaultPackageManager implements PackageManager {
 	}
 
 	/**
-	 * Dedupe packages by identity. Callers pass sources in precedence order, so the
-	 * first occurrence wins.
+	 * Dedupe packages: if same package identity appears in both global and project,
+	 * keep only the project one (project wins).
 	 */
 	private dedupePackages(
 		packages: Array<{ pkg: PackageSource; scope: SourceScope }>,
@@ -1667,10 +1642,15 @@ export class DefaultPackageManager implements PackageManager {
 			const sourceStr = typeof entry.pkg === "string" ? entry.pkg : entry.pkg.source;
 			const identity = this.getPackageIdentity(sourceStr, entry.scope);
 
-			if (!seen.has(identity)) {
+			const existing = seen.get(identity);
+			if (!existing) {
+				seen.set(identity, entry);
+			} else if (entry.scope === "project" && existing.scope === "user") {
+				// Project wins over user
 				seen.set(identity, entry);
 			}
-			// Callers pass sources in precedence order. Keep the first matching identity.
+			// If existing is project and new is global, keep existing (project)
+			// If both are same scope, keep first one
 		}
 
 		return Array.from(seen.values());
@@ -1748,9 +1728,6 @@ export class DefaultPackageManager implements PackageManager {
 	}
 
 	private async installNpm(source: NpmSource, scope: SourceScope, temporary: boolean): Promise<void> {
-		if (scope === "projectUser") {
-			this.ensureProjectUserRootIgnore();
-		}
 		const installRoot = this.getNpmInstallRoot(scope, temporary);
 		this.ensureNpmProject(installRoot);
 		await this.runNpmCommand(this.getNpmInstallArgs([source.spec], installRoot));
@@ -1769,9 +1746,6 @@ export class DefaultPackageManager implements PackageManager {
 	}
 
 	private async installGit(source: GitSource, scope: SourceScope): Promise<void> {
-		if (scope === "projectUser") {
-			this.ensureProjectUserRootIgnore();
-		}
 		const targetDir = this.getGitInstallPath(source, scope);
 		if (existsSync(targetDir)) {
 			if (source.ref) {
@@ -1907,17 +1881,10 @@ export class DefaultPackageManager implements PackageManager {
 		}
 	}
 
-	private ensureProjectUserRootIgnore(): void {
-		ensureIgnoredProjectUserConfigDir(join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME));
-	}
-
 	private getNpmInstallRoot(scope: SourceScope, temporary: boolean): string {
 		if (temporary) {
 			return this.getTemporaryDir("npm");
 		}
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "npm");
-		}
 		if (scope === "project") {
 			return join(this.cwd, CONFIG_DIR_NAME, "npm");
 		}
@@ -1958,9 +1925,6 @@ export class DefaultPackageManager implements PackageManager {
 		if (scope === "temporary") {
 			return join(this.getTemporaryDir("npm"), "node_modules", source.name);
 		}
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "npm", "node_modules", source.name);
-		}
 		if (scope === "project") {
 			return join(this.cwd, CONFIG_DIR_NAME, "npm", "node_modules", source.name);
 		}
@@ -1988,22 +1952,17 @@ export class DefaultPackageManager implements PackageManager {
 		if (scope === "temporary") {
 			return this.getTemporaryDir(`git-${source.host}`, source.path);
 		}
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "git", source.host, source.path);
+		const installRoot = this.getGitInstallRoot(scope);
+		if (!installRoot) {
+			throw new Error("Missing git install root");
 		}
-		if (scope === "project") {
-			return join(this.cwd, CONFIG_DIR_NAME, "git", source.host, source.path);
-		}
-		return join(this.agentDir, "git", source.host, source.path);
+		return this.resolveManagedPath(installRoot, source.host, source.path);
 	}
 
 	private getGitInstallRoot(scope: SourceScope): string | undefined {
 		if (scope === "temporary") {
 			return undefined;
 		}
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "git");
-		}
 		if (scope === "project") {
 			return join(this.cwd, CONFIG_DIR_NAME, "git");
 		}
@@ -2011,17 +1970,24 @@ export class DefaultPackageManager implements PackageManager {
 	}
 
 	private getTemporaryDir(prefix: string, suffix?: string): string {
+		const root = this.resolveManagedPath(join(tmpdir(), "pi-extensions"), prefix);
 		const hash = createHash("sha256")
 			.update(`${prefix}-${suffix ?? ""}`)
 			.digest("hex")
 			.slice(0, 8);
-		return join(tmpdir(), "pi-extensions", prefix, hash, suffix ?? "");
+		return this.resolveManagedPath(root, hash, suffix ?? "");
+	}
+
+	private resolveManagedPath(root: string, ...parts: string[]): string {
+		const resolvedRoot = resolve(root);
+		const resolvedPath = resolve(resolvedRoot, ...parts);
+		if (resolvedPath !== resolvedRoot && !resolvedPath.startsWith(`${resolvedRoot}${sep}`)) {
+			throw new Error(`Refusing to use path outside package install root: ${resolvedPath}`);
+		}
+		return resolvedPath;
 	}
 
 	private getBaseDirForScope(scope: SourceScope): string {
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME);
-		}
 		if (scope === "project") {
 			return join(this.cwd, CONFIG_DIR_NAME);
 		}
@@ -2241,8 +2207,9 @@ export class DefaultPackageManager implements PackageManager {
 	private addAutoDiscoveredResources(
 		accumulator: ResourceAccumulator,
 		globalSettings: ReturnType<SettingsManager["getGlobalSettings"]>,
-		projectLayers: ReturnType<SettingsManager["getProjectSettingsLayers"]>,
+		projectSettings: ReturnType<SettingsManager["getProjectSettings"]>,
 		globalBaseDir: string,
+		projectBaseDir: string,
 	): void {
 		const userMetadata: PathMetadata = {
 			source: "auto",
@@ -2250,11 +2217,11 @@ export class DefaultPackageManager implements PackageManager {
 			origin: "top-level",
 			baseDir: globalBaseDir,
 		};
-		const projectAgentMetadata: PathMetadata = {
+		const projectMetadata: PathMetadata = {
 			source: "auto",
 			scope: "project",
 			origin: "top-level",
-			baseDir: join(this.cwd, CONFIG_DIR_NAME),
+			baseDir: projectBaseDir,
 		};
 
 		const userOverrides = {
@@ -2263,11 +2230,11 @@ export class DefaultPackageManager implements PackageManager {
 			prompts: (globalSettings.prompts ?? []) as string[],
 			themes: (globalSettings.themes ?? []) as string[],
 		};
-		const projectSkillOverrides = [...projectLayers]
-			.reverse()
-			.reduce<string[]>((skills, layer) => layer.settings.skills ?? skills, []);
-		const projectAgentOverrides = {
-			skills: projectSkillOverrides,
+		const projectOverrides = {
+			extensions: (projectSettings.extensions ?? []) as string[],
+			skills: (projectSettings.skills ?? []) as string[],
+			prompts: (projectSettings.prompts ?? []) as string[],
+			themes: (projectSettings.themes ?? []) as string[],
 		};
 
 		const userDirs = {
@@ -2276,6 +2243,12 @@ export class DefaultPackageManager implements PackageManager {
 			prompts: join(globalBaseDir, "prompts"),
 			themes: join(globalBaseDir, "themes"),
 		};
+		const projectDirs = {
+			extensions: join(projectBaseDir, "extensions"),
+			skills: join(projectBaseDir, "skills"),
+			prompts: join(projectBaseDir, "prompts"),
+			themes: join(projectBaseDir, "themes"),
+		};
 		const userAgentsSkillsDir = join(getHomeDir(), ".agents", "skills");
 		const projectAgentsSkillDirs = collectAncestorAgentsSkillDirs(this.cwd).filter(
 			(dir) => resolve(dir) !== resolve(userAgentsSkillsDir),
@@ -2295,73 +2268,55 @@ export class DefaultPackageManager implements PackageManager {
 			}
 		};
 
-		for (const layer of projectLayers) {
-			const projectBaseDir = this.getBaseDirForScope(layer.scope);
-			const projectMetadata: PathMetadata = {
-				source: "auto",
-				scope: layer.scope,
-				origin: "top-level",
-				baseDir: projectBaseDir,
-			};
-			const projectOverrides = {
-				extensions: (layer.settings.extensions ?? []) as string[],
-				skills: (layer.settings.skills ?? []) as string[],
-				prompts: (layer.settings.prompts ?? []) as string[],
-				themes: (layer.settings.themes ?? []) as string[],
-			};
-			const projectDirs = {
-				extensions: join(projectBaseDir, "extensions"),
-				skills: join(projectBaseDir, "skills"),
-				prompts: join(projectBaseDir, "prompts"),
-				themes: join(projectBaseDir, "themes"),
-			};
+		// Project extensions from .pi/
+		addResources(
+			"extensions",
+			collectAutoExtensionEntries(projectDirs.extensions),
+			projectMetadata,
+			projectOverrides.extensions,
+			projectBaseDir,
+		);
 
-			addResources(
-				"extensions",
-				collectAutoExtensionEntries(projectDirs.extensions),
-				projectMetadata,
-				projectOverrides.extensions,
-				projectBaseDir,
-			);
-			addResources(
-				"skills",
-				collectAutoSkillEntries(projectDirs.skills, "pi"),
-				projectMetadata,
-				projectOverrides.skills,
-				projectBaseDir,
-			);
-			addResources(
-				"prompts",
-				collectAutoPromptEntries(projectDirs.prompts),
-				projectMetadata,
-				projectOverrides.prompts,
-				projectBaseDir,
-			);
-			addResources(
-				"themes",
-				collectAutoThemeEntries(projectDirs.themes),
-				projectMetadata,
-				projectOverrides.themes,
-				projectBaseDir,
-			);
-		}
+		// Project skills from .pi/
+		addResources(
+			"skills",
+			collectAutoSkillEntries(projectDirs.skills, "pi"),
+			projectMetadata,
+			projectOverrides.skills,
+			projectBaseDir,
+		);
 
 		// Project skills from .agents/ (each with its own baseDir)
 		for (const agentsSkillsDir of projectAgentsSkillDirs) {
 			const agentsBaseDir = dirname(agentsSkillsDir); // the .agents directory
 			const agentsMetadata: PathMetadata = {
-				...projectAgentMetadata,
+				...projectMetadata,
 				baseDir: agentsBaseDir,
 			};
 			addResources(
 				"skills",
 				collectAutoSkillEntries(agentsSkillsDir, "agents"),
 				agentsMetadata,
-				projectAgentOverrides.skills,
+				projectOverrides.skills,
 				agentsBaseDir,
 			);
 		}
 
+		addResources(
+			"prompts",
+			collectAutoPromptEntries(projectDirs.prompts),
+			projectMetadata,
+			projectOverrides.prompts,
+			projectBaseDir,
+		);
+		addResources(
+			"themes",
+			collectAutoThemeEntries(projectDirs.themes),
+			projectMetadata,
+			projectOverrides.themes,
+			projectBaseDir,
+		);
+
 		// User extensions from ~/.pi/agent/
 		addResources(
 			"extensions",

packages/coding-agent/src/core/project-user-config.ts

@@ -1,14 +0,0 @@
-import { existsSync, mkdirSync, writeFileSync } from "node:fs";
-import { join } from "node:path";
-
-export const PROJECT_USER_GITIGNORE_CONTENT = "*\n.*\n";
-
-export function ensureIgnoredProjectUserConfigDir(dir: string): void {
-	if (!existsSync(dir)) {
-		mkdirSync(dir, { recursive: true });
-	}
-	const ignorePath = join(dir, ".gitignore");
-	if (!existsSync(ignorePath)) {
-		writeFileSync(ignorePath, PROJECT_USER_GITIGNORE_CONTENT, "utf-8");
-	}
-}

packages/coding-agent/src/core/resource-loader.ts

@@ -1,7 +1,7 @@
 import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
 import { join, resolve, sep } from "node:path";
 import chalk from "chalk";
-import { CONFIG_DIR_NAME, PROJECT_USER_CONFIG_DIR_NAME } from "../config.ts";
+import { CONFIG_DIR_NAME } from "../config.ts";
 import { loadThemeFromPath, type Theme } from "../modes/interactive/theme/theme.ts";
 import type { ResourceDiagnostic } from "./diagnostics.ts";
 
@@ -652,10 +652,6 @@ export class DefaultResourceLoader implements ResourceLoader {
 			join(this.agentDir, "extensions"),
 		];
 		const projectRoots = [
-			join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "skills"),
-			join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "prompts"),
-			join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "themes"),
-			join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "extensions"),
 			join(this.cwd, CONFIG_DIR_NAME, "skills"),
 			join(this.cwd, CONFIG_DIR_NAME, "prompts"),
 			join(this.cwd, CONFIG_DIR_NAME, "themes"),
@@ -858,13 +854,9 @@ export class DefaultResourceLoader implements ResourceLoader {
 	}
 
 	private discoverSystemPromptFile(): string | undefined {
-		const projectPaths = this.settingsManager.isProjectConfigTrusted()
-			? [join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "SYSTEM.md"), join(this.cwd, CONFIG_DIR_NAME, "SYSTEM.md")]
-			: [];
-		for (const projectPath of projectPaths) {
-			if (existsSync(projectPath)) {
-				return projectPath;
-			}
+		const projectPath = join(this.cwd, CONFIG_DIR_NAME, "SYSTEM.md");
+		if (this.settingsManager.isProjectConfigTrusted() && existsSync(projectPath)) {
+			return projectPath;
 		}
 
 		const globalPath = join(this.agentDir, "SYSTEM.md");
@@ -876,16 +868,9 @@ export class DefaultResourceLoader implements ResourceLoader {
 	}
 
 	private discoverAppendSystemPromptFile(): string | undefined {
-		const projectPaths = this.settingsManager.isProjectConfigTrusted()
-			? [
-					join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME, "APPEND_SYSTEM.md"),
-					join(this.cwd, CONFIG_DIR_NAME, "APPEND_SYSTEM.md"),
-				]
-			: [];
-		for (const projectPath of projectPaths) {
-			if (existsSync(projectPath)) {
-				return projectPath;
-			}
+		const projectPath = join(this.cwd, CONFIG_DIR_NAME, "APPEND_SYSTEM.md");
+		if (this.settingsManager.isProjectConfigTrusted() && existsSync(projectPath)) {
+			return projectPath;
 		}
 
 		const globalPath = join(this.agentDir, "APPEND_SYSTEM.md");

packages/coding-agent/src/core/settings-manager.ts

@@ -2,10 +2,9 @@ import type { Transport } from "@earendil-works/pi-ai";
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
 import { dirname, join } from "path";
 import lockfile from "proper-lockfile";
-import { CONFIG_DIR_NAME, getAgentDir, PROJECT_USER_CONFIG_DIR_NAME } from "../config.ts";
+import { CONFIG_DIR_NAME, getAgentDir } from "../config.ts";
 import { normalizePath, resolvePath } from "../utils/paths.ts";
 import { DEFAULT_HTTP_IDLE_TIMEOUT_MS, parseHttpIdleTimeoutMs } from "./http-dispatcher.ts";
-import { ensureIgnoredProjectUserConfigDir } from "./project-user-config.ts";
 
 export interface CompactionSettings {
 	enabled?: boolean; // default: true
@@ -158,18 +157,12 @@ function parseTimeoutSetting(value: unknown, settingName: string): number | unde
 	return undefined;
 }
 
-export type SettingsScope = "global" | "project" | "projectUser";
-export type ProjectSettingsScope = "project" | "projectUser";
+export type SettingsScope = "global" | "project";
 
 export interface SettingsManagerCreateOptions {
 	projectConfigTrusted?: boolean;
 }
 
-export interface ProjectSettingsLayer {
-	scope: ProjectSettingsScope;
-	settings: Settings;
-}
-
 export interface SettingsStorage {
 	withLock(scope: SettingsScope, fn: (current: string | undefined) => string | undefined): void;
 	setProjectConfigTrusted?(trusted: boolean): void;
@@ -184,7 +177,6 @@ export interface SettingsError {
 export class FileSettingsStorage implements SettingsStorage {
 	private globalSettingsPath: string;
 	private projectSettingsPath: string;
-	private projectUserSettingsPath: string;
 	private projectConfigTrusted: boolean;
 
 	constructor(cwd: string, agentDir: string, options: SettingsManagerCreateOptions = {}) {
@@ -192,7 +184,6 @@ export class FileSettingsStorage implements SettingsStorage {
 		const resolvedAgentDir = resolvePath(agentDir);
 		this.globalSettingsPath = join(resolvedAgentDir, "settings.json");
 		this.projectSettingsPath = join(resolvedCwd, CONFIG_DIR_NAME, "settings.json");
-		this.projectUserSettingsPath = join(resolvedCwd, PROJECT_USER_CONFIG_DIR_NAME, "settings.json");
 		this.projectConfigTrusted = options.projectConfigTrusted ?? true;
 	}
 
@@ -231,24 +222,13 @@ export class FileSettingsStorage implements SettingsStorage {
 		throw (lastError as Error) ?? new Error("Failed to acquire settings lock");
 	}
 
-	private getSettingsPath(scope: SettingsScope): string {
-		switch (scope) {
-			case "global":
-				return this.globalSettingsPath;
-			case "project":
-				return this.projectSettingsPath;
-			case "projectUser":
-				return this.projectUserSettingsPath;
-		}
-	}
-
 	withLock(scope: SettingsScope, fn: (current: string | undefined) => string | undefined): void {
-		if ((scope === "project" || scope === "projectUser") && !this.projectConfigTrusted) {
+		if (scope === "project" && !this.projectConfigTrusted) {
 			fn(undefined);
 			return;
 		}
 
-		const path = this.getSettingsPath(scope);
+		const path = scope === "global" ? this.globalSettingsPath : this.projectSettingsPath;
 		const dir = dirname(path);
 
 		let release: (() => void) | undefined;
@@ -262,9 +242,7 @@ export class FileSettingsStorage implements SettingsStorage {
 			const next = fn(current);
 			if (next !== undefined) {
 				// Only create directory when we actually need to write
-				if (scope === "projectUser") {
-					ensureIgnoredProjectUserConfigDir(dir);
-				} else if (!existsSync(dir)) {
+				if (!existsSync(dir)) {
 					mkdirSync(dir, { recursive: true });
 				}
 				if (!release) {
@@ -283,7 +261,6 @@ export class FileSettingsStorage implements SettingsStorage {
 export class InMemorySettingsStorage implements SettingsStorage {
 	private global: string | undefined;
 	private project: string | undefined;
-	private projectUser: string | undefined;
 	private projectConfigTrusted = true;
 
 	setProjectConfigTrusted(trusted: boolean): void {
@@ -295,20 +272,18 @@ export class InMemorySettingsStorage implements SettingsStorage {
 	}
 
 	withLock(scope: SettingsScope, fn: (current: string | undefined) => string | undefined): void {
-		if ((scope === "project" || scope === "projectUser") && !this.projectConfigTrusted) {
+		if (scope === "project" && !this.projectConfigTrusted) {
 			fn(undefined);
 			return;
 		}
 
-		const current = scope === "global" ? this.global : scope === "project" ? this.project : this.projectUser;
+		const current = scope === "global" ? this.global : this.project;
 		const next = fn(current);
 		if (next !== undefined) {
 			if (scope === "global") {
 				this.global = next;
-			} else if (scope === "project") {
-				this.project = next;
 			} else {
-				this.projectUser = next;
+				this.project = next;
 			}
 		}
 	}
@@ -318,18 +293,14 @@ export class SettingsManager {
 	private storage: SettingsStorage;
 	private globalSettings: Settings;
 	private projectSettings: Settings;
-	private projectUserSettings: Settings;
 	private settings: Settings;
 	private projectConfigTrusted: boolean;
 	private modifiedFields = new Set<keyof Settings>(); // Track global fields modified during session
 	private modifiedNestedFields = new Map<keyof Settings, Set<string>>(); // Track global nested field modifications
 	private modifiedProjectFields = new Set<keyof Settings>(); // Track project fields modified during session
 	private modifiedProjectNestedFields = new Map<keyof Settings, Set<string>>(); // Track project nested field modifications
-	private modifiedProjectUserFields = new Set<keyof Settings>(); // Track .pi.user fields modified during session
-	private modifiedProjectUserNestedFields = new Map<keyof Settings, Set<string>>(); // Track .pi.user nested field modifications
 	private globalSettingsLoadError: Error | null = null; // Track if global settings file had parse errors
 	private projectSettingsLoadError: Error | null = null; // Track if project settings file had parse errors
-	private projectUserSettingsLoadError: Error | null = null; // Track if .pi.user settings file had parse errors
 	private writeQueue: Promise<void> = Promise.resolve();
 	private errors: SettingsError[];
 
@@ -337,35 +308,19 @@ export class SettingsManager {
 		storage: SettingsStorage,
 		initialGlobal: Settings,
 		initialProject: Settings,
-		initialProjectUser: Settings,
 		globalLoadError: Error | null = null,
 		projectLoadError: Error | null = null,
-		projectUserLoadError: Error | null = null,
 		initialErrors: SettingsError[] = [],
 		projectConfigTrusted = true,
 	) {
 		this.storage = storage;
 		this.globalSettings = initialGlobal;
 		this.projectSettings = initialProject;
-		this.projectUserSettings = initialProjectUser;
 		this.projectConfigTrusted = projectConfigTrusted;
 		this.globalSettingsLoadError = globalLoadError;
 		this.projectSettingsLoadError = projectLoadError;
-		this.projectUserSettingsLoadError = projectUserLoadError;
 		this.errors = [...initialErrors];
-		this.settings = this.mergeAllSettings();
-	}
-
-	private mergeProjectSettings(): Settings {
-		return deepMergeSettings(this.projectSettings, this.projectUserSettings);
-	}
-
-	private mergeAllSettings(): Settings {
-		return deepMergeSettings(this.globalSettings, this.mergeProjectSettings());
-	}
-
-	private rebuildSettings(): void {
-		this.settings = this.mergeAllSettings();
+		this.settings = deepMergeSettings(this.globalSettings, this.projectSettings);
 	}
 
 	/** Create a SettingsManager that loads from files */
@@ -383,7 +338,6 @@ export class SettingsManager {
 		const projectConfigTrusted = storage.isProjectConfigTrusted?.() ?? true;
 		const globalLoad = SettingsManager.tryLoadFromStorage(storage, "global");
 		const projectLoad = SettingsManager.tryLoadFromStorage(storage, "project");
-		const projectUserLoad = SettingsManager.tryLoadFromStorage(storage, "projectUser");
 		const initialErrors: SettingsError[] = [];
 		if (globalLoad.error) {
 			initialErrors.push({ scope: "global", error: globalLoad.error });
@@ -391,18 +345,13 @@ export class SettingsManager {
 		if (projectLoad.error) {
 			initialErrors.push({ scope: "project", error: projectLoad.error });
 		}
-		if (projectUserLoad.error) {
-			initialErrors.push({ scope: "projectUser", error: projectUserLoad.error });
-		}
 
 		return new SettingsManager(
 			storage,
 			globalLoad.settings,
 			projectLoad.settings,
-			projectUserLoad.settings,
 			globalLoad.error,
 			projectLoad.error,
-			projectUserLoad.error,
 			initialErrors,
 			projectConfigTrusted,
 		);
@@ -511,20 +460,6 @@ export class SettingsManager {
 		return structuredClone(this.projectSettings);
 	}
 
-	getProjectUserSettings(): Settings {
-		return structuredClone(this.projectUserSettings);
-	}
-
-	getProjectSettingsLayers(): ProjectSettingsLayer[] {
-		if (!this.projectConfigTrusted) {
-			return [];
-		}
-		return [
-			{ scope: "projectUser", settings: structuredClone(this.projectUserSettings) },
-			{ scope: "project", settings: structuredClone(this.projectSettings) },
-		];
-	}
-
 	isProjectConfigTrusted(): boolean {
 		return this.projectConfigTrusted;
 	}
@@ -534,14 +469,10 @@ export class SettingsManager {
 		this.storage.setProjectConfigTrusted?.(trusted);
 		if (!trusted) {
 			this.projectSettings = {};
-			this.projectUserSettings = {};
 			this.projectSettingsLoadError = null;
-			this.projectUserSettingsLoadError = null;
 			this.modifiedProjectFields.clear();
 			this.modifiedProjectNestedFields.clear();
-			this.modifiedProjectUserFields.clear();
-			this.modifiedProjectUserNestedFields.clear();
-			this.rebuildSettings();
+			this.settings = deepMergeSettings(this.globalSettings, this.projectSettings);
 		}
 	}
 
@@ -560,8 +491,6 @@ export class SettingsManager {
 		this.modifiedNestedFields.clear();
 		this.modifiedProjectFields.clear();
 		this.modifiedProjectNestedFields.clear();
-		this.modifiedProjectUserFields.clear();
-		this.modifiedProjectUserNestedFields.clear();
 
 		const projectLoad = SettingsManager.tryLoadFromStorage(this.storage, "project");
 		if (!projectLoad.error) {
@@ -572,16 +501,7 @@ export class SettingsManager {
 			this.recordError("project", projectLoad.error);
 		}
 
-		const projectUserLoad = SettingsManager.tryLoadFromStorage(this.storage, "projectUser");
-		if (!projectUserLoad.error) {
-			this.projectUserSettings = projectUserLoad.settings;
-			this.projectUserSettingsLoadError = null;
-		} else {
-			this.projectUserSettingsLoadError = projectUserLoad.error;
-			this.recordError("projectUser", projectUserLoad.error);
-		}
-
-		this.rebuildSettings();
+		this.settings = deepMergeSettings(this.globalSettings, this.projectSettings);
 	}
 
 	/** Apply additional overrides on top of current settings */
@@ -611,17 +531,6 @@ export class SettingsManager {
 		}
 	}
 
-	/** Mark a .pi.user field as modified during this session */
-	private markProjectUserModified(field: keyof Settings, nestedKey?: string): void {
-		this.modifiedProjectUserFields.add(field);
-		if (nestedKey) {
-			if (!this.modifiedProjectUserNestedFields.has(field)) {
-				this.modifiedProjectUserNestedFields.set(field, new Set());
-			}
-			this.modifiedProjectUserNestedFields.get(field)!.add(nestedKey);
-		}
-	}
-
 	private recordError(scope: SettingsScope, error: unknown): void {
 		const normalizedError = error instanceof Error ? error : new Error(String(error));
 		this.errors.push({ scope, error: normalizedError });
@@ -633,14 +542,9 @@ export class SettingsManager {
 			this.modifiedNestedFields.clear();
 			return;
 		}
-		if (scope === "project") {
-			this.modifiedProjectFields.clear();
-			this.modifiedProjectNestedFields.clear();
-			return;
-		}
 
-		this.modifiedProjectUserFields.clear();
-		this.modifiedProjectUserNestedFields.clear();
+		this.modifiedProjectFields.clear();
+		this.modifiedProjectNestedFields.clear();
 	}
 
 	private enqueueWrite(scope: SettingsScope, task: () => void): void {
@@ -694,7 +598,7 @@ export class SettingsManager {
 	}
 
 	private save(): void {
-		this.rebuildSettings();
+		this.settings = deepMergeSettings(this.globalSettings, this.projectSettings);
 
 		if (this.globalSettingsLoadError) {
 			return;
@@ -711,7 +615,7 @@ export class SettingsManager {
 
 	private saveProjectSettings(settings: Settings): void {
 		this.projectSettings = structuredClone(settings);
-		this.rebuildSettings();
+		this.settings = deepMergeSettings(this.globalSettings, this.projectSettings);
 
 		if (this.projectSettingsLoadError) {
 			return;
@@ -725,22 +629,6 @@ export class SettingsManager {
 		});
 	}
 
-	private saveProjectUserSettings(settings: Settings): void {
-		this.projectUserSettings = structuredClone(settings);
-		this.rebuildSettings();
-
-		if (this.projectUserSettingsLoadError) {
-			return;
-		}
-
-		const snapshotProjectUserSettings = structuredClone(this.projectUserSettings);
-		const modifiedFields = new Set(this.modifiedProjectUserFields);
-		const modifiedNestedFields = this.cloneModifiedNestedFields(this.modifiedProjectUserNestedFields);
-		this.enqueueWrite("projectUser", () => {
-			this.persistScopedSettings("projectUser", snapshotProjectUserSettings, modifiedFields, modifiedNestedFields);
-		});
-	}
-
 	async flush(): Promise<void> {
 		await this.writeQueue;
 	}
@@ -1017,13 +905,6 @@ export class SettingsManager {
 		this.saveProjectSettings(projectSettings);
 	}
 
-	setProjectUserPackages(packages: PackageSource[]): void {
-		const projectUserSettings = structuredClone(this.projectUserSettings);
-		projectUserSettings.packages = packages;
-		this.markProjectUserModified("packages");
-		this.saveProjectUserSettings(projectUserSettings);
-	}
-
 	getExtensionPaths(): string[] {
 		return [...(this.settings.extensions ?? [])];
 	}
@@ -1041,13 +922,6 @@ export class SettingsManager {
 		this.saveProjectSettings(projectSettings);
 	}
 
-	setProjectUserExtensionPaths(paths: string[]): void {
-		const projectUserSettings = structuredClone(this.projectUserSettings);
-		projectUserSettings.extensions = paths;
-		this.markProjectUserModified("extensions");
-		this.saveProjectUserSettings(projectUserSettings);
-	}
-
 	getSkillPaths(): string[] {
 		return [...(this.settings.skills ?? [])];
 	}
@@ -1065,13 +939,6 @@ export class SettingsManager {
 		this.saveProjectSettings(projectSettings);
 	}
 
-	setProjectUserSkillPaths(paths: string[]): void {
-		const projectUserSettings = structuredClone(this.projectUserSettings);
-		projectUserSettings.skills = paths;
-		this.markProjectUserModified("skills");
-		this.saveProjectUserSettings(projectUserSettings);
-	}
-
 	getPromptTemplatePaths(): string[] {
 		return [...(this.settings.prompts ?? [])];
 	}
@@ -1089,13 +956,6 @@ export class SettingsManager {
 		this.saveProjectSettings(projectSettings);
 	}
 
-	setProjectUserPromptTemplatePaths(paths: string[]): void {
-		const projectUserSettings = structuredClone(this.projectUserSettings);
-		projectUserSettings.prompts = paths;
-		this.markProjectUserModified("prompts");
-		this.saveProjectUserSettings(projectUserSettings);
-	}
-
 	getThemePaths(): string[] {
 		return [...(this.settings.themes ?? [])];
 	}
@@ -1113,13 +973,6 @@ export class SettingsManager {
 		this.saveProjectSettings(projectSettings);
 	}
 
-	setProjectUserThemePaths(paths: string[]): void {
-		const projectUserSettings = structuredClone(this.projectUserSettings);
-		projectUserSettings.themes = paths;
-		this.markProjectUserModified("themes");
-		this.saveProjectUserSettings(projectUserSettings);
-	}
-
 	getEnableSkillCommands(): boolean {
 		return this.settings.enableSkillCommands ?? true;
 	}

packages/coding-agent/src/core/slash-commands.ts

@@ -36,6 +36,6 @@ export const BUILTIN_SLASH_COMMANDS: ReadonlyArray<BuiltinSlashCommand> = [
 	{ name: "compact", description: "Manually compact the session context" },
 	{ name: "resume", description: "Resume a different session" },
 	{ name: "reload", description: "Reload keybindings, extensions, skills, prompts, and themes" },
-	{ name: "trust", description: "Configure project .pi/.pi.user trust" },
+	{ name: "trust", description: "Configure project .pi trust" }
 	{ name: "quit", description: `Quit ${APP_NAME}` },
 ];

packages/coding-agent/src/core/source-info.ts

@@ -15,7 +15,7 @@ export function createSourceInfo(path: string, metadata: PathMetadata): SourceIn
 	return {
 		path,
 		source: metadata.source,
-		scope: metadata.scope === "projectUser" ? "project" : metadata.scope,
+		scope: metadata.scope,
 		origin: metadata.origin,
 		baseDir: metadata.baseDir,
 	};

packages/coding-agent/src/core/trust-manager.ts

@@ -1,7 +1,7 @@
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
 import lockfile from "proper-lockfile";
-import { CONFIG_DIR_NAME, PROJECT_USER_CONFIG_DIR_NAME } from "../config.ts";
+import { CONFIG_DIR_NAME } from "../config.ts";
 import { canonicalizePath, resolvePath } from "../utils/paths.ts";
 
 export type ProjectTrustDecision = boolean | null;
@@ -53,7 +53,7 @@ function writeTrustFile(path: string, data: TrustFile): void {
 
 export function hasProjectConfig(cwd: string): boolean {
 	const resolvedCwd = resolvePath(cwd);
-	return existsSync(join(resolvedCwd, CONFIG_DIR_NAME)) || existsSync(join(resolvedCwd, PROJECT_USER_CONFIG_DIR_NAME));
+	return existsSync(join(resolvedCwd, CONFIG_DIR_NAME));
 }
 
 export class ProjectTrustStore {

packages/coding-agent/src/index.ts

@@ -152,15 +152,12 @@ export type { ReadonlyFooterDataProvider } from "./core/footer-data-provider.ts"
 export { convertToLlm } from "./core/messages.ts";
 export { ModelRegistry } from "./core/model-registry.ts";
 export type {
-	InstalledSourceScope,
 	PackageManager,
 	PathMetadata,
 	ProgressCallback,
 	ProgressEvent,
 	ResolvedPaths,
 	ResolvedResource,
-	ResourceMetadataScope,
-	SettingsSourceScope,
 } from "./core/package-manager.ts";
 export { DefaultPackageManager } from "./core/package-manager.ts";
 export type { ResourceCollision, ResourceDiagnostic, ResourceLoader } from "./core/resource-loader.ts";
@@ -220,8 +217,6 @@ export {
 	type CompactionSettings,
 	type ImageSettings,
 	type PackageSource,
-	type ProjectSettingsLayer,
-	type ProjectSettingsScope,
 	type RetrySettings,
 	SettingsManager,
 	type SettingsManagerCreateOptions,

packages/coding-agent/src/main.ts

@@ -508,7 +508,7 @@ interface ProjectTrustPromptResult {
 async function promptForProjectTrust(cwd: string, settingsManager: SettingsManager): Promise<ProjectTrustPromptResult> {
 	const selected = await showStartupSelector(
 		settingsManager,
-		`Trust project configuration?\nLoad .pi and .pi.user from ${cwd}?\nWarning: Project extensions can execute code.`,
+		`Trust project configuration?\nLoad .pi from ${cwd}?\nWarning: Project extensions can execute code.`,
 		[
 			{ label: "Yes (remember)", value: { trusted: true, remember: true } },
 			{ label: "Yes (this session)", value: { trusted: true, remember: false } },

packages/coding-agent/src/modes/interactive/components/config-selector.ts

@@ -15,7 +15,7 @@ import {
 	truncateToWidth,
 	visibleWidth,
 } from "@earendil-works/pi-tui";
-import { CONFIG_DIR_NAME, PROJECT_USER_CONFIG_DIR_NAME } from "../../../config.ts";
+import { CONFIG_DIR_NAME } from "../../../config.ts";
 import type { PathMetadata, ResolvedPaths, ResolvedResource } from "../../../core/package-manager.ts";
 import type { PackageSource, SettingsManager } from "../../../core/settings-manager.ts";
 import { theme } from "../theme/theme.ts";
@@ -50,7 +50,7 @@ interface ResourceSubgroup {
 interface ResourceGroup {
 	key: string;
 	label: string;
-	scope: PathMetadata["scope"];
+	scope: "user" | "project" | "temporary";
 	origin: "package" | "top-level";
 	source: string;
 	subgroups: ResourceSubgroup[];
@@ -75,29 +75,18 @@ function formatBaseDir(baseDir: string): string {
 
 function getGroupLabel(metadata: PathMetadata): string {
 	if (metadata.origin === "package") {
-		return `${metadata.source} (${metadata.scope === "projectUser" ? "project user" : metadata.scope})`;
+		return `${metadata.source} (${metadata.scope})`;
 	}
 	// Top-level resources
 	if (metadata.source === "auto") {
 		if (metadata.baseDir) {
-			if (metadata.scope === "user") {
-				return `User (${formatBaseDir(metadata.baseDir)})`;
-			}
-			return metadata.scope === "projectUser"
-				? `Project user (${formatBaseDir(metadata.baseDir)})`
+			return metadata.scope === "user"
+				? `User (${formatBaseDir(metadata.baseDir)})`
 				: `Project (${formatBaseDir(metadata.baseDir)})`;
 		}
-		return metadata.scope === "user"
-			? "User (~/.pi/agent/)"
-			: metadata.scope === "projectUser"
-				? "Project user (.pi.user/)"
-				: "Project (.pi/)";
+		return metadata.scope === "user" ? "User (~/.pi/agent/)" : "Project (.pi/)";
 	}
-	return metadata.scope === "user"
-		? "User settings"
-		: metadata.scope === "projectUser"
-			? "Project user settings"
-			: "Project settings";
+	return metadata.scope === "user" ? "User settings" : "Project settings";
 }
 
 function buildGroups(resolved: ResolvedPaths): ResourceGroup[] {
@@ -159,15 +148,14 @@ function buildGroups(resolved: ResolvedPaths): ResourceGroup[] {
 	addToGroup(resolved.prompts, "prompts");
 	addToGroup(resolved.themes, "themes");
 
-	// Sort groups: packages first, then top-level; user before project.
-	const scopeOrder: Record<PathMetadata["scope"], number> = { user: 0, projectUser: 1, project: 2, temporary: 3 };
+	// Sort groups: packages first, then top-level; user before project
 	const groups = Array.from(groupMap.values());
 	groups.sort((a, b) => {
 		if (a.origin !== b.origin) {
 			return a.origin === "package" ? -1 : 1;
 		}
 		if (a.scope !== b.scope) {
-			return scopeOrder[a.scope] - scopeOrder[b.scope];
+			return a.scope === "user" ? -1 : 1;
 		}
 		return a.source.localeCompare(b.source);
 	});
@@ -466,27 +454,10 @@ class ResourceList implements Component, Focusable {
 		}
 	}
 
-	private getSettingsScope(item: ResourceItem): "user" | "project" | "projectUser" {
-		return item.metadata.scope === "projectUser"
-			? "projectUser"
-			: item.metadata.scope === "project"
-				? "project"
-				: "user";
-	}
-
-	private getSettingsForScope(scope: "user" | "project" | "projectUser") {
-		if (scope === "projectUser") {
-			return this.settingsManager.getProjectUserSettings();
-		}
-		if (scope === "project") {
-			return this.settingsManager.getProjectSettings();
-		}
-		return this.settingsManager.getGlobalSettings();
-	}
-
 	private toggleTopLevelResource(item: ResourceItem, enabled: boolean): void {
-		const scope = this.getSettingsScope(item);
-		const settings = this.getSettingsForScope(scope);
+		const scope = item.metadata.scope as "user" | "project";
+		const settings =
+			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
 
 		const arrayKey = item.resourceType as "extensions" | "skills" | "prompts" | "themes";
 		const current = (settings[arrayKey] ?? []) as string[];
@@ -508,17 +479,7 @@ class ResourceList implements Component, Focusable {
 			updated.push(disablePattern);
 		}
 
-		if (scope === "projectUser") {
-			if (arrayKey === "extensions") {
-				this.settingsManager.setProjectUserExtensionPaths(updated);
-			} else if (arrayKey === "skills") {
-				this.settingsManager.setProjectUserSkillPaths(updated);
-			} else if (arrayKey === "prompts") {
-				this.settingsManager.setProjectUserPromptTemplatePaths(updated);
-			} else if (arrayKey === "themes") {
-				this.settingsManager.setProjectUserThemePaths(updated);
-			}
-		} else if (scope === "project") {
+		if (scope === "project") {
 			if (arrayKey === "extensions") {
 				this.settingsManager.setProjectExtensionPaths(updated);
 			} else if (arrayKey === "skills") {
@@ -542,8 +503,9 @@ class ResourceList implements Component, Focusable {
 	}
 
 	private togglePackageResource(item: ResourceItem, enabled: boolean): void {
-		const scope = this.getSettingsScope(item);
-		const settings = this.getSettingsForScope(scope);
+		const scope = item.metadata.scope as "user" | "project";
+		const settings =
+			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
 
 		const packages = [...(settings.packages ?? [])] as PackageSource[];
 		const pkgIndex = packages.findIndex((pkg) => {
@@ -592,24 +554,19 @@ class ResourceList implements Component, Focusable {
 			packages[pkgIndex] = (pkg as { source: string }).source;
 		}
 
-		if (scope === "projectUser") {
-			this.settingsManager.setProjectUserPackages(packages);
-		} else if (scope === "project") {
+		if (scope === "project") {
 			this.settingsManager.setProjectPackages(packages);
 		} else {
 			this.settingsManager.setPackages(packages);
 		}
 	}
 
-	private getTopLevelBaseDir(scope: "user" | "project" | "projectUser"): string {
-		if (scope === "projectUser") {
-			return join(this.cwd, PROJECT_USER_CONFIG_DIR_NAME);
-		}
+	private getTopLevelBaseDir(scope: "user" | "project"): string {
 		return scope === "project" ? join(this.cwd, CONFIG_DIR_NAME) : this.agentDir;
 	}
 
 	private getResourcePattern(item: ResourceItem): string {
-		const scope = this.getSettingsScope(item);
+		const scope = item.metadata.scope as "user" | "project";
 		const baseDir = item.metadata.baseDir ?? this.getTopLevelBaseDir(scope);
 		return relative(baseDir, item.path);
 	}

packages/coding-agent/src/modes/interactive/interactive-mode.ts

@@ -4954,7 +4954,7 @@ export class InteractiveMode {
 		const cwd = this.sessionManager.getCwd();
 		const current = this.formatTrustDecision(trustStore.get(cwd));
 		const choice = await this.showExtensionSelector(
-			`Trust project configuration?\nCurrent setting: ${current}\nLoad .pi and .pi.user from ${cwd}?\nWarning: Project extensions can execute code.`,
+			`Trust project configuration?\nCurrent setting: ${current}\nLoad .pi from ${cwd}?\nWarning: Project extensions can execute code.`,
 			["Yes (remember)", "Yes (this session)", "No (remember)", "No (this session)"],
 		);
 		if (choice === "Yes (remember)") {

packages/coding-agent/src/package-manager-cli.ts

@@ -48,7 +48,6 @@ interface PackageCommandOptions {
 	source?: string;
 	updateTarget?: UpdateTarget;
 	local: boolean;
-	localUser: boolean;
 	force: boolean;
 	help: boolean;
 	invalidOption?: string;
@@ -75,9 +74,9 @@ function reportSettingsErrors(settingsManager: SettingsManager, context: string)
 function getPackageCommandUsage(command: PackageCommand): string {
 	switch (command) {
 		case "install":
-			return `${APP_NAME} install <source> [-l] [-u]`;
+			return `${APP_NAME} install <source> [-l]`;
 		case "remove":
-			return `${APP_NAME} remove <source> [-l] [-u]`;
+			return `${APP_NAME} remove <source> [-l]`;
 		case "update":
 			return `${APP_NAME} update [source|self|pi] [--self] [--extensions] [--extension <source>] [--force]`;
 		case "list":
@@ -95,7 +94,6 @@ Install a package and add it to settings.
 
 Options:
   -l, --local    Install project-locally (.pi/settings.json)
-  -u, --user     With --local, write to .pi.user/settings.json instead
   -f, --force    Trust project config for this command
 
 Examples:
@@ -113,11 +111,10 @@ Examples:
   ${getPackageCommandUsage("remove")}
 
 Remove a package and its source from settings.
-Alias: ${APP_NAME} uninstall <source> [-l] [-u]
+Alias: ${APP_NAME} uninstall <source> [-l]
 
 Options:
   -l, --local    Remove from project settings (.pi/settings.json)
-  -u, --user     With --local, remove from .pi.user/settings.json instead
   -f, --force    Trust project config for this command
 
 Examples:
@@ -171,7 +168,6 @@ function parsePackageCommand(args: string[]): PackageCommandOptions | undefined
 	}
 
 	let local = false;
-	let localUser = false;
 	let force = false;
 	let help = false;
 	let invalidOption: string | undefined;
@@ -199,15 +195,6 @@ function parsePackageCommand(args: string[]): PackageCommandOptions | undefined
 			continue;
 		}
 
-		if (arg === "-u" || arg === "--user") {
-			if (command === "install" || command === "remove") {
-				localUser = true;
-			} else {
-				invalidOption = invalidOption ?? arg;
-			}
-			continue;
-		}
-
 		if (arg === "--self") {
 			if (command === "update") {
 				selfFlag = true;
@@ -294,16 +281,11 @@ function parsePackageCommand(args: string[]): PackageCommandOptions | undefined
 		}
 	}
 
-	if (localUser && !local) {
-		conflictingOptions = conflictingOptions ?? "--user can only be used with --local";
-	}
-
 	return {
 		command,
 		source,
 		updateTarget,
 		local,
-		localUser,
 		force,
 		help,
 		invalidOption,
@@ -525,15 +507,12 @@ export async function handlePackageCommand(
 	try {
 		switch (options.command) {
 			case "install":
-				await packageManager.installAndPersist(source!, { local: options.local, localUser: options.localUser });
+				await packageManager.installAndPersist(source!, { local: options.local });
 				console.log(chalk.green(`Installed ${source}`));
 				return true;
 
 			case "remove": {
-				const removed = await packageManager.removeAndPersist(source!, {
-					local: options.local,
-					localUser: options.localUser,
-				});
+				const removed = await packageManager.removeAndPersist(source!, { local: options.local });
 				if (!removed) {
 					console.error(chalk.red(`No matching package found for ${source}`));
 					process.exitCode = 1;
@@ -547,7 +526,6 @@ export async function handlePackageCommand(
 				const configuredPackages = packageManager.listConfiguredPackages();
 				const userPackages = configuredPackages.filter((pkg) => pkg.scope === "user");
 				const projectPackages = configuredPackages.filter((pkg) => pkg.scope === "project");
-				const projectUserPackages = configuredPackages.filter((pkg) => pkg.scope === "projectUser");
 
 				if (configuredPackages.length === 0) {
 					console.log(chalk.dim("No packages installed."));
@@ -577,14 +555,6 @@ export async function handlePackageCommand(
 					}
 				}
 
-				if (projectUserPackages.length > 0) {
-					if (userPackages.length > 0 || projectPackages.length > 0) console.log();
-					console.log(chalk.bold("Project user packages:"));
-					for (const pkg of projectUserPackages) {
-						formatPackage(pkg);
-					}
-				}
-
 				return true;
 			}
 

packages/coding-agent/test/package-command-paths.test.ts

@@ -171,7 +171,7 @@ describe("package commands", () => {
 
 			const stderr = errorSpy.mock.calls.map(([message]) => String(message)).join("\n");
 			expect(stderr).toContain('Unknown option --unknown for "install".');
-			expect(stderr).toContain('Use "pi --help" or "pi install <source> [-l] [-u]".');
+			expect(stderr).toContain('Use "pi --help" or "pi install <source> [-l]".');
 			expect(process.exitCode).toBe(1);
 		} finally {
 			errorSpy.mockRestore();

packages/coding-agent/test/package-manager.test.ts

@@ -1,5 +1,5 @@
 import { EventEmitter } from "node:events";
-import { existsSync, mkdirSync, readFileSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
+import { mkdirSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join, relative } from "node:path";
 import { PassThrough } from "node:stream";
@@ -33,6 +33,10 @@ interface PackageManagerInternals {
 		options?: { cwd?: string; timeoutMs?: number; env?: Record<string, string> },
 	): Promise<string>;
 	getLocalGitUpdateTarget(installedPath: string): Promise<{ ref: string; head: string; fetchArgs: string[] }>;
+	getGitInstallPath(
+		source: { type: "git"; repo: string; host: string; path: string; pinned: boolean; ref?: string },
+		scope: "user" | "project" | "temporary",
+	): string;
 }
 
 // Helper to check if a resource is enabled
@@ -156,38 +160,6 @@ Content`,
 			expect(result.extensions.some((r) => r.path === extPath && r.enabled)).toBe(true);
 		});
 
-		it("should resolve project user paths relative to .pi.user", async () => {
-			const extDir = join(tempDir, ".pi.user", "extensions");
-			mkdirSync(extDir, { recursive: true });
-			const extPath = join(extDir, "project-user-ext.ts");
-			writeFileSync(extPath, "export default function() {}");
-
-			settingsManager.setProjectUserExtensionPaths(["extensions/project-user-ext.ts"]);
-
-			const result = await packageManager.resolve();
-			const ext = result.extensions.find((r) => r.path === extPath);
-			expect(ext?.enabled).toBe(true);
-			expect(ext?.metadata.scope).toBe("projectUser");
-		});
-
-		it("should prefer .pi.user resources over .pi resources", async () => {
-			const projectExtDir = join(tempDir, ".pi", "extensions");
-			const projectUserExtDir = join(tempDir, ".pi.user", "extensions");
-			mkdirSync(projectExtDir, { recursive: true });
-			mkdirSync(projectUserExtDir, { recursive: true });
-			const projectExtPath = join(projectExtDir, "shared.ts");
-			const projectUserExtPath = join(projectUserExtDir, "shared.ts");
-			writeFileSync(projectExtPath, "export default function() {}");
-			writeFileSync(projectUserExtPath, "export default function() {}");
-
-			const result = await packageManager.resolve();
-			const sharedPaths = result.extensions.filter((r) => r.path.endsWith("shared.ts"));
-
-			expect(sharedPaths).toHaveLength(2);
-			expect(sharedPaths[0].path).toBe(projectUserExtPath);
-			expect(sharedPaths[1].path).toBe(projectExtPath);
-		});
-
 		it("should auto-discover user prompts with overrides", async () => {
 			const promptsDir = join(agentDir, "prompts");
 			mkdirSync(promptsDir, { recursive: true });
@@ -740,21 +712,6 @@ Content`,
 			);
 		});
 
-		it("should create ignored .pi.user folder for project user npm installs", async () => {
-			expect(existsSync(join(tempDir, ".pi.user"))).toBe(false);
-			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
-			const runCommandSpy = vi.spyOn(managerWithInternals, "runCommand").mockResolvedValue(undefined);
-
-			await packageManager.install("npm:@scope/pkg", { local: true, localUser: true });
-
-			expect(readFileSync(join(tempDir, ".pi.user", ".gitignore"), "utf-8")).toBe("*\n.*\n");
-			expect(runCommandSpy).toHaveBeenCalledWith(
-				"npm",
-				["install", "@scope/pkg", "--prefix", join(tempDir, ".pi.user", "npm"), "--legacy-peer-deps"],
-				undefined,
-			);
-		});
-
 		it("should use bun --cwd for npm package installs", async () => {
 			settingsManager = SettingsManager.inMemory({
 				npmCommand: ["mise", "exec", "bun@1", "--", "bun"],
@@ -1185,6 +1142,25 @@ Content`,
 		});
 	});
 
+	describe("git install paths", () => {
+		it("should reject paths outside git install roots", () => {
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			const traversalSource = {
+				type: "git" as const,
+				repo: "git@evil.example:../../victim/repo",
+				host: "evil.example",
+				path: "../../victim/repo",
+				pinned: false,
+			};
+
+			for (const scope of ["user", "project", "temporary"] as const) {
+				expect(() => managerWithInternals.getGitInstallPath(traversalSource, scope)).toThrow(
+					"outside package install root",
+				);
+			}
+		});
+	});
+
 	describe("settings source normalization", () => {
 		it("should store global local packages relative to agent settings base", () => {
 			const pkgDir = join(tempDir, "packages", "local-global-pkg");
@@ -1214,23 +1190,6 @@ Content`,
 			expect(settings.packages?.[0]).toBe(expected);
 		});
 
-		it("should store project user local packages relative to .pi.user settings base", () => {
-			const projectPkgDir = join(tempDir, "project-user-local-pkg");
-			mkdirSync(join(projectPkgDir, "extensions"), { recursive: true });
-			writeFileSync(join(projectPkgDir, "extensions", "index.ts"), "export default function() {}");
-
-			const added = packageManager.addSourceToSettings("./project-user-local-pkg", {
-				local: true,
-				localUser: true,
-			});
-			expect(added).toBe(true);
-
-			const settings = settingsManager.getProjectUserSettings();
-			const rel = relative(join(tempDir, ".pi.user"), projectPkgDir);
-			const expected = rel.startsWith(".") ? rel : `./${rel}`;
-			expect(settings.packages?.[0]).toBe(expected);
-		});
-
 		it("should remove local package entries using equivalent path forms", () => {
 			const pkgDir = join(tempDir, "remove-local-pkg");
 			mkdirSync(join(pkgDir, "extensions"), { recursive: true });

packages/coding-agent/test/resource-loader.test.ts

@@ -329,19 +329,6 @@ Content`,
 			expect(loader.getSystemPrompt()).toBe("You are a helpful assistant.");
 		});
 
-		it("should prefer SYSTEM.md from cwd/.pi.user", async () => {
-			const piDir = join(cwd, ".pi");
-			const piUserDir = join(cwd, ".pi.user");
-			mkdirSync(piDir, { recursive: true });
-			mkdirSync(piUserDir, { recursive: true });
-			writeFileSync(join(piDir, "SYSTEM.md"), "Project system prompt.");
-			writeFileSync(join(piUserDir, "SYSTEM.md"), "Project user system prompt.");
-
-			const loader = new DefaultResourceLoader({ cwd, agentDir });
-			await loader.reload();
-
-			expect(loader.getSystemPrompt()).toBe("Project user system prompt.");
-		});
 
 		it("should skip .pi SYSTEM.md when project config is not trusted", async () => {
 			const piDir = join(cwd, ".pi");

packages/coding-agent/test/settings-manager.test.ts

@@ -258,43 +258,15 @@ describe("SettingsManager", () => {
 		});
 	});
 
-	describe("project user settings", () => {
-		it("should let .pi.user override .pi and global settings", () => {
-			writeFileSync(join(agentDir, "settings.json"), JSON.stringify({ theme: "global" }));
-			writeFileSync(join(projectDir, ".pi", "settings.json"), JSON.stringify({ theme: "project" }));
-			mkdirSync(join(projectDir, ".pi.user"), { recursive: true });
-			writeFileSync(join(projectDir, ".pi.user", "settings.json"), JSON.stringify({ theme: "project-user" }));
-
-			const manager = SettingsManager.create(projectDir, agentDir);
-
-			expect(manager.getTheme()).toBe("project-user");
-			expect(manager.getProjectSettings().theme).toBe("project");
-			expect(manager.getProjectUserSettings().theme).toBe("project-user");
-		});
-
+	describe("project config trust", () => {
 		it("should skip project settings when project config is not trusted", () => {
 			writeFileSync(join(agentDir, "settings.json"), JSON.stringify({ theme: "global" }));
 			writeFileSync(join(projectDir, ".pi", "settings.json"), JSON.stringify({ theme: "project" }));
-			mkdirSync(join(projectDir, ".pi.user"), { recursive: true });
-			writeFileSync(join(projectDir, ".pi.user", "settings.json"), JSON.stringify({ theme: "project-user" }));
 
 			const manager = SettingsManager.create(projectDir, agentDir, { projectConfigTrusted: false });
 
 			expect(manager.getTheme()).toBe("global");
 			expect(manager.getProjectSettings()).toEqual({});
-			expect(manager.getProjectUserSettings()).toEqual({});
-			expect(manager.getProjectSettingsLayers()).toEqual([]);
-		});
-
-		it("should create ignored .pi.user folder when writing project user settings", async () => {
-			rmSync(join(projectDir, ".pi.user"), { recursive: true, force: true });
-			const manager = SettingsManager.create(projectDir, agentDir);
-
-			manager.setProjectUserPackages(["npm:test-pkg"]);
-			await manager.flush();
-
-			expect(existsSync(join(projectDir, ".pi.user", "settings.json"))).toBe(true);
-			expect(readFileSync(join(projectDir, ".pi.user", ".gitignore"), "utf-8")).toBe("*\n.*\n");
 		});
 	});
 

packages/coding-agent/test/trust-manager.test.ts

@@ -1,4 +1,4 @@
-import { existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { mkdirSync, readFileSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
@@ -43,15 +43,10 @@ describe("ProjectTrustStore", () => {
 		expect(readFileSync(trustPath, "utf-8")).toBe("{not json");
 	});
 
-	it("detects .pi and .pi.user project config directories", () => {
+	it("detects .pi project config directories", () => {
 		expect(hasProjectConfig(cwd)).toBe(false);
 
 		mkdirSync(join(cwd, ".pi"), { recursive: true });
 		expect(hasProjectConfig(cwd)).toBe(true);
-
-		rmSync(join(cwd, ".pi"), { recursive: true, force: true });
-		mkdirSync(join(cwd, ".pi.user"), { recursive: true });
-		expect(hasProjectConfig(cwd)).toBe(true);
-		expect(existsSync(join(cwd, ".pi.user"))).toBe(true);
 	});
 });