apex-code 0.0.1-alpha.8 → 0.0.4

package/docs/extensions.md

@@ -330,7 +330,8 @@ user sends another prompt ◄─────────────────
 
 /compact or auto-compaction
   ├─► session_before_compact (can cancel or customize)
-  └─► session_compact
+  ├─► session_compact (success)
+  └─► session_compact_failed (failure or abort)
 
 /tree navigation
   ├─► session_before_tree (can cancel or customize)
@@ -448,7 +449,7 @@ pi.on("session_before_fork", async (event, ctx) => {
 After a successful fork or clone, Apex Code emits `session_shutdown` for the old extension instance, reloads and rebinds extensions for the new session, then emits `session_start` with `reason: "fork"` and `previousSessionFile`.
 Do cleanup work in `session_shutdown`, then reestablish any in-memory state in `session_start`.
 
-#### session_before_compact / session_compact
+#### session_before_compact / session_compact / session_compact_failed
 
 Fired on compaction. See [compaction.md](compaction.md) for details.
 
@@ -479,6 +480,14 @@ pi.on("session_compact", async (event, ctx) => {
   // event.reason - "manual" (/compact), "threshold", or "overflow"
   // event.willRetry - whether the aborted turn is retried after compaction (overflow recovery)
 });
+
+pi.on("session_compact_failed", async (event, ctx) => {
+  // event.reason - "manual" (/compact), "threshold", or "overflow"
+  // event.errorMessage - present for non-abort failures
+  // event.aborted - true for cancelled/aborted compactions
+  // event.willRetry - whether the aborted turn would have retried after compaction
+  // event.fromExtension - whether extension-provided compaction content was being used
+});
 ```
 
 #### session_before_tree / session_tree
@@ -571,6 +580,24 @@ pi.on("agent_settled", async (_event, ctx) => {
 });
 ```
 
+#### ui_prompt_start / ui_prompt_end
+
+Notification-only lifecycle events for blocking user-facing extension UI prompts. They fire around `ctx.ui.select()`, `ctx.ui.confirm()`, `ctx.ui.input()`, `ctx.ui.editor()`, and `ctx.ui.custom()` so host/status integrations can report "waiting for user" instead of just "running".
+
+Nested or overlapping prompts are coalesced into one outer waiting span. Handlers are invoked best-effort and are not awaited before showing or closing the prompt.
+
+```typescript
+pi.on("ui_prompt_start", async (event, ctx) => {
+  // event.reason === "ui_prompt"
+  // event.kind: "select" | "confirm" | "input" | "editor" | "custom"
+  // event.title: prompt title when available
+});
+
+pi.on("ui_prompt_end", async (event, ctx) => {
+  // Pi is no longer waiting on that UI prompt span.
+});
+```
+
 #### turn_start / turn_end
 
 Fired for each turn (one LLM response + tool calls).
@@ -2050,7 +2077,7 @@ pi.registerTool({
 
 ### Overriding Built-in Tools
 
-Extensions can override built-in tools (`read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`) by registering a tool with the same name. Interactive mode displays a warning when this happens.
+Extensions can override built-in tools (`read`, `bash`, `powershell`, `edit`, `write`, `grep`, `find`, `ls`) by registering a tool with the same name. Interactive mode displays a warning when this happens.
 
 ```bash
 # Extension's read tool replaces built-in read
@@ -2074,6 +2101,7 @@ See [examples/extensions/tool-override.ts](../examples/extensions/tool-override.
 Built-in tool implementations:
 - [read.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/read.ts) - `ReadToolDetails`
 - [bash.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/bash.ts) - `BashToolDetails`
+- [powershell.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/powershell.ts) - `PowerShellToolDetails`
 - [edit.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/edit.ts)
 - [write.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/write.ts)
 - [grep.ts](https://github.com/Fchery87/apex-code/blob/main/packages/coding-agent/src/core/tools/grep.ts) - `GrepToolDetails`
@@ -2109,11 +2137,11 @@ pi.registerTool({
 });
 ```
 
-**Operations interfaces:** `ReadOperations`, `WriteOperations`, `EditOperations`, `BashOperations`, `LsOperations`, `GrepOperations`, `FindOperations`
+**Operations interfaces:** `ReadOperations`, `WriteOperations`, `EditOperations`, `BashOperations`, `PowerShellOperations`, `LsOperations`, `GrepOperations`, `FindOperations`
 
 For `user_bash`, extensions can reuse Apex Code's local shell backend via `createLocalBashOperations()` instead of reimplementing local process spawning, shell resolution, and process-tree termination.
 
-The bash tool also supports a spawn hook to adjust the command, cwd, or env before execution:
+The `bash` and `powershell` tools also support a spawn hook to adjust the command, cwd, or env before execution:
 
 ```typescript
 import { createBashTool } from "apex-code";
@@ -2127,7 +2155,7 @@ const bashTool = createBashTool(cwd, {
 });
 ```
 
-`createBashTool()` exposes the current session to commands through `PI_SESSION_ID`, `PI_SESSION_FILE`, `PI_PROVIDER`, `PI_MODEL`, and `PI_REASONING_LEVEL`. Injection happens before `spawnHook`, so hooks receive these values in `env` and preserve them when they spread the existing environment as above. Set `exposeSessionEnvironment: false` to disable them:
+`createBashTool()` and `createPowerShellTool()` expose the current session to commands through `PI_SESSION_ID`, `PI_SESSION_FILE`, `PI_PROVIDER`, `PI_MODEL`, and `PI_REASONING_LEVEL`. Injection happens before `spawnHook`, so hooks receive these values in `env` and preserve them when they spread the existing environment as above. Set `exposeSessionEnvironment: false` to disable them:
 
 ```typescript
 const bashTool = createBashTool(cwd, {
@@ -2135,7 +2163,7 @@ const bashTool = createBashTool(cwd, {
 });
 ```
 
-See [Bash tool session environment](environment-variables.md#bash-tool-session-environment) for variable semantics. See [examples/extensions/ssh.ts](../examples/extensions/ssh.ts) for a complete SSH example with `--ssh` flag.
+See [Shell tool session environment](environment-variables.md#shell-tool-session-environment) for variable semantics. See [examples/extensions/ssh.ts](../examples/extensions/ssh.ts) for a complete SSH example with `--ssh` flag.
 
 ### Output Truncation
 

package/docs/json.md

@@ -15,12 +15,16 @@ except that streaming message updates omit cumulative snapshots:
 ```typescript
 type WithoutPartial<T> = T extends { partial: unknown } ? Omit<T, "partial"> : T;
 
+type JsonAssistantMessageEvent<T> = T extends { type: "toolcall_start"; partial: unknown }
+  ? WithoutPartial<T> & { id: string; toolName: string }
+  : WithoutPartial<T>;
+
 type JsonAgentSessionEvent =
   | Exclude<AgentSessionEvent, { type: "message_update" }>
   | {
       type: "message_update";
       usage: Usage;
-      assistantMessageEvent: WithoutPartial<AssistantMessageEvent>;
+      assistantMessageEvent: JsonAssistantMessageEvent<AssistantMessageEvent>;
     };
 ```
 
@@ -84,7 +88,8 @@ Followed by events as they occur:
 `assistantMessageEvent.partial` to keep stream size linear. The top-level `usage` field contains
 the latest cumulative provider-reported usage and may remain zero when a provider only reports
 usage at completion. Use `contentIndex` and `delta` to assemble live text, thinking, or tool-call
-arguments if needed. `message_end` contains the final authoritative message.
+arguments if needed. A `toolcall_start` event also includes the constant-sized `id` and `toolName`
+fields. `message_end` contains the final authoritative message.
 
 ## Example
 

package/docs/keybindings.md

@@ -70,7 +70,7 @@ The dedicated history actions always change history entries, regardless of the c
 |--------|---------|-------------|
 | `tui.editor.yank` | `ctrl+y` | Paste most recently deleted text |
 | `tui.editor.yankPop` | `alt+y` | Cycle through deleted text after yank |
-| `tui.editor.undo` | `ctrl+-` | Undo last edit |
+| `tui.editor.undo` | `ctrl+-` (`ctrl+z` on Windows; `alt+z` on WSL) | Undo last edit |
 
 ### TUI Clipboard and Selection
 
@@ -107,9 +107,9 @@ This routing remains configurable through the ordinary action bindings. For exam
 | `tui.altScreen.halfPageDown` | *(none)* | Scroll the transcript down by half a page |
 | `tui.altScreen.lineUp` | *(none)* | Scroll the transcript up by one line |
 | `tui.altScreen.lineDown` | *(none)* | Scroll the transcript down by one line |
-| `tui.altScreen.previousPrompt` | `ctrl+shift+up` | Jump to the previous marked message |
-| `tui.altScreen.nextPrompt` | `ctrl+shift+down` | Jump to the next marked message |
-| `tui.altScreen.search` | `ctrl+shift+f` | Search the rendered transcript |
+| `tui.altScreen.previousPrompt` | `ctrl+shift+up`, `ctrl+up` (`ctrl+up` only on Windows and WSL) | Jump to the previous marked message |
+| `tui.altScreen.nextPrompt` | `ctrl+shift+down`, `ctrl+down` (`ctrl+down` only on Windows and WSL) | Jump to the next marked message |
+| `tui.altScreen.search` | `ctrl+shift+f` (`ctrl+f` on Windows and WSL) | Search the rendered transcript |
 | `tui.altScreen.searchNext` | `enter`, `ctrl+g` | Select the next search match while searching |
 | `tui.altScreen.searchPrevious` | `shift+enter`, `ctrl+shift+g` | Select the previous search match while searching |
 | `tui.altScreen.searchClose` | `escape` | Close transcript search |
@@ -125,7 +125,7 @@ This routing remains configurable through the ordinary action bindings. For exam
 | `app.exit` | `ctrl+d` | Exit (when editor empty) |
 | `app.suspend` | `ctrl+z` (none on Windows) | Suspend to background |
 | `app.editor.external` | `ctrl+g` | Open in external editor (`externalEditor`, `$VISUAL`, `$EDITOR`, Notepad on Windows, or `nano` elsewhere) |
-| `app.clipboard.pasteImage` | `ctrl+v` (`alt+v` on Windows) | Paste image or text from clipboard |
+| `app.clipboard.pasteImage` | `ctrl+v` (`alt+v` on Windows and WSL) | Paste image or text from clipboard |
 
 ### Sessions
 
@@ -148,7 +148,7 @@ This routing remains configurable through the ordinary action bindings. For exam
 |--------|---------|-------------|
 | `app.model.select` | `ctrl+l` | Open model selector |
 | `app.model.cycleForward` | `ctrl+p` | Cycle to next model |
-| `app.model.cycleBackward` | `shift+ctrl+p` | Cycle to previous model |
+| `app.model.cycleBackward` | `shift+ctrl+p` (`alt+p` on Windows and WSL) | Cycle to previous model |
 | `app.thinking.cycle` | `shift+tab` | Cycle thinking level |
 | `app.thinking.toggle` | `ctrl+t` | Collapse or expand thinking blocks |
 
@@ -157,9 +157,9 @@ This routing remains configurable through the ordinary action bindings. For exam
 | Keybinding id | Default | Description |
 |--------|---------|-------------|
 | `app.tools.expand` | `ctrl+o` | Collapse or expand tool output |
-| `app.message.copy` | `ctrl+x` | Copy the last assistant message, or the selected message in `/tree` |
-| `app.message.followUp` | `alt+enter` | Queue follow-up message |
-| `app.message.dequeue` | `alt+up` | Restore queued messages to editor |
+| `app.message.copy` | `ctrl+x` | Copy the selected message in `/tree`; otherwise copy the last assistant message, or the active fullscreen text selection when `fullscreenCopyOnSelect` is disabled |
+| `app.message.followUp` | `alt+enter` (`ctrl+q` on Windows and WSL) | Queue follow-up message |
+| `app.message.dequeue` | `alt+up` (`alt+q` on Windows and WSL) | Restore queued messages to editor |
 
 ### Tree Navigation
 

package/docs/llama-cpp.md

@@ -53,6 +53,8 @@ Start Apex Code and configure the provider:
 
 Enter the router URL and optional API key. The default URL is `http://127.0.0.1:8080`.
 
+If you start the router with `--no-models-autoload`, `/login llama.cpp` only stores the connection. Run `/llama` to load a model, then `/model` to select the loaded model for the current session.
+
 Environment variables can configure the same values without `/login`:
 
 ```bash

package/docs/models.md

@@ -254,6 +254,8 @@ Current behavior:
 
 Only OpenAI-compatible APIs apply it (`openai-completions`, `openai-responses`, `azure-openai-responses`); other APIs ignore it. Keys override Apex Code's named request fields (for example a `temperature` key here beats the request-level temperature), so prefer it as the single source of sampling truth for a model. In `modelOverrides`, `samplingParams` merges per key with the base model's value.
 
+A constant thinking-token cap can go here too, but it will not follow `thinkingBudgets` or leave room for the answer. Prefer `compat.thinkingTokenBudgetField` (or the `supportsThinkingTokenBudget` alias) for that.
+
 ### Thinking Level Map
 
 Use `thinkingLevelMap` on a model to describe model-specific thinking controls. Keys are Apex Code thinking levels: `off`, `minimal`, `low`, `medium`, `high`, `xhigh`, `max`. Maps may contain holes; for example, a model can expose `high` and `max` without exposing `xhigh`.
@@ -467,8 +469,10 @@ For providers with partial OpenAI compatibility, use the `compat` field.
 | `requiresThinkingAsText` | Convert thinking blocks to plain text |
 | `requiresReasoningContentOnAssistantMessages` | Include empty `reasoning_content` on all replayed assistant messages when reasoning is enabled |
 | `thinkingFormat` | Use `reasoning_effort`, `openrouter`, `deepseek`, `together`, `baseten`, `zai`, `qwen`, `chat-template`, or `qwen-chat-template` thinking parameters |
-| `chatTemplateKwargs` | `chat_template_kwargs` values for `thinkingFormat: "chat-template"`; use `{ "$var": "thinking.enabled" }` or `{ "$var": "thinking.effort" }` for Apex Code-controlled thinking values |
-| `chatTemplateArgs` | `chat_template_args` values for `thinkingFormat: "baseten"`; use `{ "$var": "thinking.enabled" }` or `{ "$var": "thinking.effort" }` for Apex Code-controlled thinking values |
+| `chatTemplateKwargs` | `chat_template_kwargs` values for `thinkingFormat: "chat-template"`; use `{ "$var": "thinking.enabled" }`, `{ "$var": "thinking.effort" }`, or `{ "$var": "thinking.budget" }` for Apex Code-controlled thinking values |
+| `chatTemplateArgs` | `chat_template_args` values for `thinkingFormat: "baseten"`; use `{ "$var": "thinking.enabled" }`, `{ "$var": "thinking.effort" }`, or `{ "$var": "thinking.budget" }` for Apex Code-controlled thinking values |
+| `thinkingTokenBudgetField` | Top-level request field used to cap reasoning tokens from `thinkingBudgets`, clamped so at least 1024 tokens remain for the answer. `"thinking_token_budget"` (vLLM), `"thinking_budget"` (Qwen/DashScope/SGLang), `"thinking_budget_tokens"` (llama.cpp). Off by default; not set on the generated catalog. |
+| `supportsThinkingTokenBudget` | Alias for `thinkingTokenBudgetField: "thinking_token_budget"` (vLLM). Prefer `thinkingTokenBudgetField`. Default: `false`. |
 | `cacheControlFormat` | Use Anthropic-style `cache_control` markers on the system prompt, last tool definition, and last user, assistant, or tool-result text content. Currently only `anthropic` is supported. |
 | `sendSessionAffinityHeaders` | For `openai-completions`, send session-affinity headers from the session id when caching is enabled. Default: `false`. |
 | `sessionAffinityFormat` | For `openai-completions` and `openai-responses`, the session-affinity header format: `openai` sends `session_id`/`x-client-request-id` (completions also `x-session-affinity`), `openai-nosession` omits the underscore-containing `session_id` header, `openrouter` sends `x-session-id`. Does not affect the `prompt_cache_key` body param. Default: auto-detected. |
@@ -481,6 +485,8 @@ For providers with partial OpenAI compatibility, use the `compat` field.
 
 `openrouter` uses `reasoning: { effort }`. `together` uses `reasoning: { enabled }` and also `reasoning_effort` when `supportsReasoningEffort` is enabled. `qwen` uses top-level `enable_thinking`. Use `qwen-chat-template` for local Qwen-compatible servers that require `chat_template_kwargs.enable_thinking` and `preserve_thinking`. Use `chat-template` for vLLM/Hugging Face chat templates that need configurable `chat_template_kwargs`, such as `chatTemplateKwargs: { "thinking": { "$var": "thinking.enabled" } }` for DeepSeek V3.x templates. Use `thinkingFormat: "baseten"` with `chatTemplateArgs` for providers that expose toggle controls through `chat_template_args` and optionally support top-level `reasoning_effort`.
 
+`thinkingTokenBudgetField` is independent of `thinkingFormat`. Do not enable it on the generated Qwen catalog: those models already send `reasoning_effort`, and DashScope rejects `thinking_budget` together with `reasoning_effort`.
+
 `cacheControlFormat: "anthropic"` is for OpenAI-compatible providers that expose Anthropic-style prompt caching through `cache_control` markers on text content and tool definitions.
 
 Example:

package/docs/packages.md

@@ -38,7 +38,7 @@ apex-code update npm:@foo/bar      # update one package
 apex-code update --extension npm:@foo/bar
 ```
 
-These commands manage Apex Code packages and `apex-code update` can update the Apex Code CLI installation. To uninstall Apex Code itself, see [Quickstart](quickstart.md#uninstall).
+These commands manage Apex Code packages and `apex-code update` can update the Apex Code CLI installation. For experimental installer-managed installations, `apex-code update` installs the exact checked version into a staged, lockfile-backed release and activates it only after verification, leaving the current release intact if the update fails. Managed installations do not support `--force`; rerun the installer to repair one. To uninstall Apex Code itself, see [Quickstart](quickstart.md#uninstall).
 
 By default, `install` and `remove` write to user settings (`~/.apex-code/agent/settings.json`). Use `-l` to write to project settings (`.apex-code/settings.json`) instead. Project settings can be shared with your team, and apex-code installs any missing packages automatically on startup after the project is trusted.
 
@@ -130,7 +130,7 @@ Add a `pi` manifest to `package.json` or use conventional directories. `pi` is A
 }
 ```
 
-Paths are relative to the package root. Arrays support glob patterns and `!exclusions`.
+Paths are relative to the package root. Arrays support glob patterns and `!exclusions`. Positive manifest globs discover visible paths in lexical order. List dot-prefixed paths directly. If a glob would need to continue through a symlink, list the symlinked resource root directly.
 
 ### Gallery Metadata
 

package/docs/quickstart.md

@@ -146,7 +146,7 @@ The command output is sent to the model. Use `!!command` to run a command withou
 
 ### Switch models
 
-Use `/model` or Ctrl+L to choose a model. Use Shift+Tab to cycle thinking level. Use Ctrl+P / Shift+Ctrl+P to cycle through scoped models.
+Use `/model` or Ctrl+L to choose a model for the current session. Press Ctrl+S in the model picker to save the highlighted model as the startup default. Use `/thinking` to choose a thinking level for the current session, or Ctrl+S in that picker to save the startup default thinking level. Use Shift+Tab to cycle thinking level. Use Ctrl+P / Shift+Ctrl+P to cycle through scoped models.
 
 ### Continue later
 

package/docs/rpc.md

@@ -134,6 +134,29 @@ Response:
 {"type": "response", "command": "abort", "success": true}
 ```
 
+#### clear_queue
+
+Remove queued steering and follow-up messages and return their text.
+
+```json
+{"type": "clear_queue"}
+```
+
+Response:
+```json
+{
+  "type": "response",
+  "command": "clear_queue",
+  "success": true,
+  "data": {
+    "steering": ["Change direction"],
+    "followUp": ["Summarize when finished"]
+  }
+}
+```
+
+To implement interactive Esc behavior, send `clear_queue` before `abort`, then restore the returned text in the client editor. `abort` continues queued messages when they remain in the session.
+
 #### new_session
 
 Start a fresh session. Can be cancelled by a `session_before_switch` extension event handler.
@@ -945,7 +968,7 @@ The `assistantMessageEvent` field contains one of these delta types:
 | `thinking_start` | Thinking block started |
 | `thinking_delta` | Thinking content chunk |
 | `thinking_end` | Thinking block ended |
-| `toolcall_start` | Tool call started |
+| `toolcall_start` | Tool call started (includes `id` and `toolName`) |
 | `toolcall_delta` | Tool call arguments chunk |
 | `toolcall_end` | Tool call ended (includes full `toolCall` object) |
 
@@ -960,11 +983,17 @@ Example streaming a text response:
 The top-level `usage` field contains the latest cumulative provider-reported usage. It may remain
 zero until completion when a provider does not report usage during streaming.
 
+Example starting a tool call:
+```json
+{"type":"message_update","usage":{...},"assistantMessageEvent":{"type":"toolcall_start","contentIndex":1,"id":"call_abc123","toolName":"write"}}
+```
+
 `message_update` intentionally omits the former cumulative `message` field and
 `assistantMessageEvent.partial`. Clients that need a live partial message must assemble it
 from `message_start` and subsequent events using `contentIndex`. Treat `message_end.message`
-as authoritative. For tool calls, buffer `toolcall_delta.delta`; `toolcall_end.toolCall`
-contains the completed call.
+as authoritative. For tool calls, `toolcall_start` provides the call `id` and `toolName`;
+buffer `toolcall_delta.delta` for arguments. `toolcall_end.toolCall` contains the completed
+call.
 
 ### bash_execution_update
 

package/docs/sdk.md

@@ -49,6 +49,31 @@ The main factory function for a single `AgentSession`.
 
 `createAgentSession()` uses a `ResourceLoader` to supply extensions, skills, prompt templates, themes, and context files. If you do not provide one, it uses `DefaultResourceLoader` with standard discovery.
 
+#### Sandbox contract
+
+The SDK cannot determine whether its host process is contained. Choose the
+contract that describes how the embedding runs:
+
+```typescript
+const { session, sandboxContract, sandboxDiagnostic } = await createAgentSession({
+  sandbox: "required",
+});
+```
+
+* `"required"` refuses to create the session unless Apex's enforcing supervisor
+  marker is present. Use this when the SDK runs inside an Apex CLI child.
+* `"external"` creates the session and reports that containment belongs to
+  another system. The SDK does not verify that system.
+* `"none"` creates the session without asserting OS containment. This is the
+  default for compatibility.
+
+The result always reports `sandboxContract`. It includes `sandboxDiagnostic` for
+`"external"` and `"none"`. Delegated children inherit the selected contract.
+Do not treat a normal SDK process, a permission gate, or a read-only tool list
+as an OS sandbox. See [ADR 0031](../../docs/adr/0031-sdk-sandbox-contract.md)
+and [ADR 0005](../../docs/adr/0005-sandbox-boundary-guarantees.md) for the
+platform limits.
+
 ```typescript
 import { createAgentSession, SessionManager } from "apex-code";
 
@@ -519,7 +544,7 @@ const { session } = await createAgentSession({ resourceLoader: loader });
 
 Specify which built-in tools to enable:
 
-- Built-in tool names: `read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`
+- Built-in tool names: `read`, `bash`, `powershell`, `edit`, `write`, `grep`, `find`, `ls`
 - Default built-ins: `read`, `bash`, `edit`, `write`
 - `noTools: "all"` disables all tools
 - `noTools: "builtin"` disables default built-ins while keeping extension and custom tools enabled
@@ -540,6 +565,11 @@ const { session } = await createAgentSession({
   tools: ["read", "bash", "grep"],
 });
 
+// Use PowerShell instead of Bash on Windows
+const { session } = await createAgentSession({
+  tools: ["read", "powershell", "edit", "write"],
+});
+
 // Disable one tool while keeping the rest available
 const { session } = await createAgentSession({
   excludeTools: ["ask_question"],
@@ -1196,7 +1226,7 @@ SettingsManager
 // Tool factories
 createCodingTools
 createReadOnlyTools
-createReadTool, createBashTool, createEditTool, createWriteTool
+createReadTool, createBashTool, createPowerShellTool, createEditTool, createWriteTool
 createGrepTool, createFindTool, createLsTool
 
 // Types

package/docs/settings.md

@@ -7,7 +7,7 @@ Apex Code uses JSON settings files with project settings overriding global setti
 | `~/.apex-code/agent/settings.json` | Global (all projects) |
 | `.apex-code/settings.json` | Project (current directory) |
 
-Edit directly or use `/settings` for common options.
+Edit directly or use `/settings` for common options. To save startup model defaults interactively, use `/model` and press Ctrl+S on the desired model. To save the startup thinking level, use `/thinking` and press Ctrl+S.
 
 ## Project Trust
 
@@ -27,12 +27,13 @@ Use `/trust` in interactive mode to save a project trust decision for future ses
 
 | Setting | Type | Default | Description |
 |---------|------|---------|-------------|
-| `defaultProvider` | string | - | Default provider (e.g., `"anthropic"`, `"openai"`) |
-| `defaultModel` | string | - | Default model ID |
-| `defaultThinkingLevel` | string | - | `"off"`, `"minimal"`, `"low"`, `"medium"`, `"high"`, `"xhigh"`, `"max"` |
+| `defaultProvider` | string | - | Startup provider (e.g., `"anthropic"`, `"openai"`; saved with Ctrl+S in `/model`, or edited manually) |
+| `defaultModel` | string | - | Startup model ID (saved with Ctrl+S in `/model`, or edited manually) |
+| `defaultThinkingLevel` | string | - | Startup thinking level (saved with Ctrl+S in `/thinking`, or edited manually): `"off"`, `"minimal"`, `"low"`, `"medium"`, `"high"`, `"xhigh"`, `"max"` |
+| `modelThinkingLevels` | object | - | Per-model startup thinking levels keyed by `"provider/modelId"`; configure from `/settings` → Default thinking level per model or edit manually |
 | `hideThinkingBlock` | boolean | `false` | Hide thinking blocks in output |
-| `showCacheMissNotices` | boolean | `false` | Show transcript notices for significant prompt-cache misses |
-| `thinkingBudgets` | object | - | Custom token budgets per thinking level |
+| `showCacheMissNotices` | boolean | `false` | Show transcript notices for significant prompt-cache misses and compaction or branch-summary usage |
+| `thinkingBudgets` | object | - | Custom token budgets per thinking level. Anthropic, Google, and Bedrock use these natively. OpenAI-compatible models use them when `compat.thinkingTokenBudgetField` (or `supportsThinkingTokenBudget`) is set. |
 
 #### thinkingBudgets
 
@@ -65,6 +66,7 @@ Use `/trust` in interactive mode to save a project trust decision for future ses
 | `tuiMode` | string | `"regular"` | Interactive TUI mode: `"regular"` or experimental `"fullscreen"`. Changes from `/settings` apply immediately; `--tui-mode` overrides this setting at startup |
 | `fullscreenExitOutput` | string | `"transcript"` | Fullscreen exit output: `"transcript"` prints the final transcript and resume hint, while `"resume-hint"` restores the previous screen and prints only the resume hint. Has no effect in regular TUI mode |
 | `fullscreenScrollbar` | string | `"auto"` | Fullscreen transcript scrollbar: `"auto"` shows it temporarily while scrolling, `"always"` reserves the rightmost column and keeps it visible, and `"hidden"` hides it. Has no effect in regular TUI mode |
+| `fullscreenCopyOnSelect` | boolean | `true` | Automatically copy selected text in fullscreen mode. When disabled, selections stay highlighted and `Ctrl+X` copies the active selection |
 
 For VS Code, include `--wait` so Apex Code resumes after the editor exits:
 
@@ -209,6 +211,9 @@ Keep `retry.provider.maxRetries` at `0` unless provider-level retries are explic
 | `terminal.showImages` | boolean | `true` | Show images in terminal (if supported) |
 | `terminal.imageWidthCells` | number | `60` | Preferred inline image width in terminal cells |
 | `terminal.clearOnShrink` | boolean | `false` | Clear empty rows when content shrinks (can cause flicker) |
+| `terminal.hyperlinks` | boolean or `"auto"` | `"auto"` | Override OSC 8 hyperlink support (advanced, JSON-only) |
+| `terminal.images` | string or boolean | `"auto"` | Override image protocol support with `"kitty"`, `"iterm2"`, `false`, or `"auto"` (advanced, JSON-only) |
+| `terminal.trueColor` | boolean or `"auto"` | `"auto"` | Override truecolor support (advanced, JSON-only) |
 | `images.autoResize` | boolean | `true` | Resize images to 2000x2000 max. Applies to `@file` attachments, `read`, and images returned by tools |
 | `images.blockImages` | boolean | `false` | Block all images from being sent to LLM |
 
@@ -248,7 +253,7 @@ Windows paths in JSON must use forward slashes or escaped backslashes:
 |---------|------|---------|-------------|
 | `defaultTools` | string[] | - | Built-in tools enabled initially. When omitted, Pi uses its standard defaults |
 
-`defaultTools` selects the built-in tools enabled at startup. Extension and SDK custom tools remain enabled:
+`defaultTools` selects the built-in tools enabled at startup. Extension and SDK custom tools remain enabled. Available built-ins are `read`, `bash`, `powershell`, `edit`, `write`, `grep`, `find`, and `ls`:
 
 ```json
 {
@@ -256,6 +261,14 @@ Windows paths in JSON must use forward slashes or escaped backslashes:
 }
 ```
 
+On Windows, select `powershell` instead of `bash`, or include both:
+
+```json
+{
+  "defaultTools": ["read", "powershell", "edit", "write"]
+}
+```
+
 An empty array starts with no built-in tools while preserving extension and SDK custom tools. `--tools` replaces this behavior with a strict allowlist for all tools, `--no-tools` disables all tools, and `--no-builtin-tools` disables the built-in defaults. `--exclude-tools` filters the resulting list. A project `defaultTools` array replaces the global array.
 
 ### Sessions
@@ -339,6 +352,9 @@ See [packages.md](packages.md) for package management details.
   "defaultProvider": "anthropic",
   "defaultModel": "claude-sonnet-4-20250514",
   "defaultThinkingLevel": "medium",
+  "modelThinkingLevels": {
+    "anthropic/claude-sonnet-4-20250514": "high"
+  },
   "theme": "dark",
   "compaction": {
     "enabled": true,

package/docs/skills.md

@@ -43,9 +43,10 @@ Apex Code loads skills from:
 > whichever of these roots they resolve under.
 
 Discovery rules:
-- In `~/.apex-code/agent/skills/` and `.apex-code/skills/`, direct root `.md` files are discovered as individual skills
+- In `~/.apex-code/agent/skills/` and `.apex-code/skills/`, direct root `.md` files are discovered as individual skills when they have valid skill frontmatter with a non-empty `description`
 - In all skill locations, directories containing `SKILL.md` are discovered recursively
-- In `~/.agents/skills/` and project `.agents/skills/`, root `.md` files are ignored
+- In `~/.agents/skills/` and project `.agents/skills/`, root `.md` files are ignored, but nested `.md` files in grouping folders are discovered when they declare skill frontmatter
+- Root Markdown files other than `SKILL.md` that do not look like skills are ignored silently
 
 Disable discovery with `--no-skills` (explicit `--skill` paths still load).
 
@@ -233,7 +234,7 @@ Apex Code validates skills against the Agent Skills standard. Most issues produc
 
 Unknown frontmatter fields are ignored.
 
-**Exception:** Skills with missing description are not loaded.
+Declared skills with missing descriptions are not loaded. Malformed `SKILL.md` files and `SKILL.md` files without a description produce warnings and are not loaded. Other Markdown files without valid skill frontmatter are ignored.
 
 Name collisions (same name from different locations) warn and keep the first skill found.
 

package/docs/terminal-setup.md

@@ -2,6 +2,18 @@
 
 Apex Code uses the [Kitty keyboard protocol](https://sw.kovidgoyal.net/kitty/keyboard-protocol/) for reliable modifier key detection. Most modern terminals support this protocol, but some require configuration.
 
+## Capability Overrides
+
+Pi auto-detects OSC 8 hyperlinks, inline image protocols, and truecolor. If detection fails behind a terminal proxy or multiplexer, use these advanced overrides:
+
+| Capability | Environment variable | JSON setting |
+|------------|----------------------|--------------|
+| OSC 8 hyperlinks | `PI_HYPERLINKS=1\|0\|auto` | `terminal.hyperlinks: true\|false\|"auto"` |
+| Inline images | `PI_IMAGE_PROTOCOL=kitty\|iterm2\|none\|auto` | `terminal.images: "kitty"\|"iterm2"\|false\|"auto"` |
+| Truecolor | `PI_TRUE_COLOR=1\|0\|auto` | `terminal.trueColor: true\|false\|"auto"` |
+
+Settings take precedence over environment variables; unset or `auto` preserves detection. Only force capabilities supported by the complete terminal path, since unsupported escape sequences can corrupt rendering.
+
 ## Kitty
 
 Works out of the box.
@@ -120,7 +132,15 @@ Add to `keybindings.json`:
 
 ## Windows Terminal
 
-Add to `settings.json` (Ctrl+Shift+, or Settings → Open JSON file) to forward the modified Enter keys Apex Code uses:
+Apex Code uses Windows-style keybindings when running natively on Windows or in WSL:
+
+- `Alt+V` pastes an image or clipboard text.
+- `Ctrl+F` searches the transcript in fullscreen mode, and `Ctrl+Up`/`Ctrl+Down` jump between marked messages.
+- `Alt+P` cycles to the previous model.
+- `Ctrl+Z` undoes editing on native Windows; WSL uses `Alt+Z` so `Ctrl+Z` can suspend Apex Code.
+- `Ctrl+Q` queues a follow-up message and `Alt+Q` restores queued messages.
+
+Add to `settings.json` (Ctrl+Shift+, or Settings → Open JSON file) to forward `Shift+Enter` for inserting a new line:
 
 ```json
 {
@@ -128,10 +148,6 @@ Add to `settings.json` (Ctrl+Shift+, or Settings → Open JSON file) to forward
     {
       "command": { "action": "sendInput", "input": "\u001b[13;2u" },
       "keys": "shift+enter"
-    },
-    {
-      "command": { "action": "sendInput", "input": "\u001b[13;3u" },
-      "keys": "alt+enter"
     }
   ]
 }
@@ -139,9 +155,9 @@ Add to `settings.json` (Ctrl+Shift+, or Settings → Open JSON file) to forward
 
 - `Shift+Enter` inserts a new line.
 - Windows Terminal binds `Alt+Enter` to fullscreen by default. That prevents Apex Code from receiving `Alt+Enter` for follow-up queueing.
-- Remapping `Alt+Enter` to `sendInput` forwards the real key chord to Apex Code instead.
+- Remapping `Alt+Enter` to `sendInput` forwards the real key chord to Apex Code instead, or configure Windows Terminal to send the key and bind `app.message.followUp` to `alt+enter` in Apex Code to use it instead of the `Ctrl+Q` default.
 
-If you already have an `actions` array, add the objects to it. If the old fullscreen behavior persists, fully close and reopen Windows Terminal.
+If you already have an `actions` array, add the object to it. Fully close and reopen Windows Terminal after changing its settings.
 
 ## xfce4-terminal, terminator
 

package/docs/usage.md

@@ -22,7 +22,7 @@ The editor can be replaced temporarily by built-in UI such as `/settings` or by
 | File reference | Type `@` to fuzzy-search project files |
 | Path completion | Press Tab to complete paths |
 | Multi-line input | Shift+Enter, or Ctrl+Enter on Windows Terminal |
-| Copy response | Ctrl+X copies the last assistant message; in `/tree`, it copies the selected message |
+| Copy response | Ctrl+X copies the selected message in `/tree`; otherwise it copies the last assistant message, or the active fullscreen text selection when `fullscreenCopyOnSelect` is disabled |
 | Images | Paste with Ctrl+V, Alt+V on Windows, or drag into the terminal |
 | Shell command | `!command` runs and sends output to the model |
 | Hidden shell command | `!!command` runs without sending output to the model |
@@ -38,9 +38,10 @@ Type `/` in the editor to open command completion. Extensions can register custo
 |---------|-------------|
 | `/login`, `/logout` | Manage OAuth or API-key credentials |
 | [`/llama`](llama-cpp.md) | Download, load, and unload llama.cpp router models |
-| `/model` | Switch models |
+| `/model` | Switch models; Ctrl+S in the picker saves the startup default |
+| `/thinking` | Switch thinking level; Ctrl+S in the picker saves the startup default |
 | `/scoped-models` | Enable/disable models for Ctrl+P cycling |
-| `/settings` | Thinking level, theme, message delivery, transport |
+| `/settings` | Theme, message delivery, transport, and other preferences |
 | `/resume` | Pick from previous sessions |
 | `/new` | Start a new session |
 | `/name <name>` | Set session display name |
@@ -142,7 +143,7 @@ If you use Apex Code for open source work and want to publish sessions for model
 ## CLI Reference
 
 ```bash
-apex-code [options] [@files...] [messages...]
+apex-code [options] [--] [@files...] [messages...]
 ```
 
 ### Package Commands
@@ -215,7 +216,7 @@ cat README.md | apex-code -p "Summarize this text"
 | `--no-builtin-tools`, `-nbt` | Disable built-in tools but keep extension/custom tools enabled |
 | `--no-tools`, `-nt` | Disable all tools |
 
-Built-in tools: `read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`.
+Built-in tools: `read`, `bash`, `powershell` (Windows), `edit`, `write`, `grep`, `find`, `ls`.
 
 ### Resource Options
 
@@ -248,6 +249,7 @@ apex-code --no-extensions -e ./my-extension.ts
 | `--verbose` | Force verbose startup |
 | `-a`, `--approve` | Trust project-local files for this run |
 | `-na`, `--no-approve` | Ignore project-local files for this run |
+| `--` | Stop option parsing; remaining arguments are prompts or `@file` inputs |
 | `-h`, `--help` | Show help |
 | `-v`, `--version` | Show version |
 
@@ -274,6 +276,9 @@ apex-code "List all .ts files in src/"
 # Non-interactive
 apex-code -p "Summarize this codebase"
 
+# Prompt beginning with a dash
+pi -p -- "- Summarize these points"
+
 # Non-interactive with piped stdin
 cat README.md | apex-code -p "Summarize this text"
 

package/docs/windows.md

@@ -1,6 +1,6 @@
 # Windows Setup
 
-Apex Code requires a bash shell on Windows. Checked locations (in order):
+Apex Code uses Git Bash by default on Windows. Checked locations (in order):
 
 1. Custom path from `~/.apex-code/agent/settings.json`
 2. Git Bash (`C:\Program Files\Git\bin\bash.exe`)
@@ -8,7 +8,29 @@ Apex Code requires a bash shell on Windows. Checked locations (in order):
 
 For most users, [Git for Windows](https://git-scm.com/download/win) is sufficient.
 
-## Custom Shell Path
+## PowerShell Tool
+
+The optional `powershell` tool runs commands through `pwsh.exe` when available, otherwise Windows PowerShell. It starts PowerShell with `-NoProfile -NonInteractive -ExecutionPolicy Bypass`. Administrator-enforced execution policies can still take precedence.
+
+Use `defaultTools` to replace the model-facing `bash` tool:
+
+```json
+{
+  "defaultTools": ["read", "powershell", "edit", "write"]
+}
+```
+
+Or enable both while comparing behavior:
+
+```json
+{
+  "defaultTools": ["read", "bash", "powershell", "edit", "write"]
+}
+```
+
+The `!` and `!!` editor commands still use Bash.
+
+## Custom Bash Path
 
 ```json
 {