@bastani/atomic 0.9.16-alpha.8 → 0.9.16

package/docs/sdk.md

@@ -102,7 +102,7 @@ The factory requires `ExecutionEnv.renameFile()` and does not add a fallback fil
 
 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.
+`createAgentSession()` uses a `ResourceLoader` to supply extensions, skills, prompt templates, themes, and context files. If you do not provide one, it uses `DefaultResourceLoader` with normal user, project, and configured-package discovery. The SDK does not add optional bundled workflow, subagent, MCP, or web-access extensions by default. It always adds the lightweight ordinary Intercom extension at the model-session boundary.
 
 ```typescript
 import { createAgentSession, SessionManager } from "@bastani/atomic";
@@ -574,20 +574,20 @@ Specify which tools to expose by name:
 
 - Built-in tool names enabled by default: `read`, `bash`, `edit`, `write`, `find`, `search`, `ask_user_question`, `todo`
 - `find` discovers filesystem paths by glob; `search` searches file contents with regex patterns across files, directories, globs, and internal URLs.
-- `tools` is an allowlist: when provided, only the listed built-in, extension, and custom tool names are exposed.
-- `excludedTools` is a blocklist: matching built-in, extension, and custom tool names are omitted from the final registry and active tool set. If both are provided, `tools` is applied first and `excludedTools` subtracts from it.
-- `noTools: "all"` disables all tools
+- `tools` is an allowlist: when provided, only the listed built-in, extension, and custom tool names are exposed, plus mandatory ordinary `intercom`.
+- `excludedTools` is a blocklist: matching built-in, extension, and custom tool names are omitted from the final registry and active tool set, except mandatory ordinary `intercom`. If both are provided, `tools` is applied first and `excludedTools` subtracts from it.
+- `noTools: "all"` disables every tool except mandatory ordinary `intercom`
 - `noTools: "builtin"` disables default built-ins while keeping extension and custom tools enabled, except names listed in `excludedTools`
 
 ```typescript
 import { createAgentSession } from "@bastani/atomic";
 
-// Read-only mode
+// Read-only mode. `tools` selects optional tools; ordinary Intercom remains active.
 const { session } = await createAgentSession({
   tools: ["read", "search", "find", "ls"],
 });
 
-// Pick specific tools
+// Pick specific optional tools. Ordinary Intercom remains active even when omitted.
 const { session } = await createAgentSession({
   tools: ["read", "bash", "search"],
 });
@@ -600,7 +600,7 @@ const { session } = await createAgentSession({
 // Allowlist first, then subtract exclusions
 const { session } = await createAgentSession({
   tools: ["read", "bash", "ask_user_question"],
-  excludedTools: ["ask_user_question"], // final tools: read, bash
+  excludedTools: ["ask_user_question"], // optional tools: read, bash; ordinary Intercom remains active
 });
 ```
 
@@ -760,6 +760,8 @@ await loader.reload();
 const { session } = await createAgentSession({ resourceLoader: loader });
 ```
 
+`createAgentSession()` preserves resources from a supplied loader but restores Atomic's mandatory bundled Intercom extension after loader overrides, deferred reloads, and same-name extension or `customTools` collisions. The supplied loader still controls every optional extension.
+
 Extensions can register tools, subscribe to events, add commands, and more. See [Extensions](/extensions) for the full API.
 
 **Event Bus:** Extensions can communicate via `pi.events`. Pass a shared `eventBus` to `DefaultResourceLoader` if you need to emit or listen from outside:

package/docs/settings.md

@@ -112,6 +112,7 @@ Chat and workflow-stage scopes are independent. Workflow stages, nested `ctx.wor
 | `theme` | string | `"dark"` | Theme name (`"dark"`, `"light"`, a Catppuccin built-in, or custom) |
 | `fullscreenScrollbar` | string | `"auto"` | Fullscreen transcript scrollbar: `"auto"` shows it temporarily while scrolling, `"always"` reserves the rightmost transcript column and keeps it visible, and `"hidden"` hides it. The thumb can be dragged when shown. |
 | `fullscreenExitOutput` | string | `"transcript"` | Fullscreen exit output: `"transcript"` prints the final transcript and session resume hint, while `"resume-hint"` restores the terminal's previous screen and prints only the resume hint. Settable from `/settings` |
+| `fullscreenCopyOnSelect` | boolean | `true` | Copy fullscreen text selections automatically on mouse release. When `false`, the selection remains highlighted and main-editor Ctrl+X copies it; Ctrl+X falls back to the last assistant message when there is no selection. Settable from `/settings` |
 | `quietStartup` | boolean | `false` | Hide startup header |
 | `defaultProjectTrust` | string | `"ask"` | Fallback project trust behavior: `"ask"`, `"always"`, or `"never"`. Global setting only |
 | `collapseChangelog` | boolean | `false` | Show condensed changelog after updates |
@@ -128,7 +129,7 @@ Chat and workflow-stage scopes are independent. Workflow stages, nested `ctx.wor
 | `autocompleteMaxVisible` | number | `5` | Max visible items in the default editor and custom editors installed through `ctx.ui.setEditorComponent()` (3-20) |
 | `showHardwareCursor` | boolean | `false` | Show the terminal cursor while TUI positions it for IME support |
 
-Interactive sessions always use the fullscreen renderer. The transcript scrolls in its own viewport while the editor, status line, usage meter, extension widgets, and footer stay docked at the bottom. Wheel and trackpad gestures go first to a focused workflow overlay, including workflow graphs and stage chats. Events that overlay does not consume fall through to the alternate-screen viewport; non-overlay focused components leave mouse input with pi-tui so transcript scrolling, scrollbar interaction, and drag selection remain available.
+Interactive sessions always use the fullscreen renderer. The transcript scrolls in its own viewport while the editor, status line, usage meter, extension widgets, and footer stay docked at the bottom. Wheel and trackpad gestures go first to a focused workflow overlay, including workflow graphs and stage chats. Events that overlay does not consume fall through to the alternate-screen viewport; non-overlay focused components leave mouse input with pi-tui so transcript scrolling, scrollbar interaction, and drag selection remain available. A selection made over a workflow overlay never copies during a hierarchy transition and is cleared when that overlay hides and the main chat repaints.
 
 The fullscreen renderer keeps minimum sizes for nested layout stacks during resize, and transient fullscreen notices stack instead of replacing a notice that is still visible.
 
@@ -284,7 +285,12 @@ Older settings with a boolean `websockets` value are migrated to `transport`: `t
 | `terminal.showTerminalProgress` | boolean | `false` | Show OSC 9;4 progress indicators in the terminal tab bar |
 | `images.autoResize` | boolean | `true` | Resize oversized images to a 2000x2000 maximum. Applies to `@file` attachments, `read`, and images returned by tools |
 | `images.blockImages` | boolean | `false` | Block all images from being sent to LLM |
+| `terminal.hyperlinks` | boolean or `"auto"` | `"auto"` | JSON-only hyperlink capability override. `true`/`false` overrides detection; `"auto"`, omitted, and invalid values preserve detection. Not shown in `/settings` |
+| `terminal.images` | `"kitty"`, `"iterm2"`, `"auto"`, or `false` | `"auto"` | JSON-only inline-image protocol override. `false` disables terminal images; `"auto"`, omitted, and invalid values preserve detection. Not shown in `/settings` |
+| `terminal.trueColor` | boolean or `"auto"` | `"auto"` | JSON-only truecolor capability override. `true`/`false` overrides detection; `"auto"`, omitted, and invalid values preserve detection. Not shown in `/settings` |
 
+
+The installed pi-tui 0.84.4 renderer owns the matching environment overrides: `PI_HYPERLINKS=1|0|auto`, `PI_IMAGE_PROTOCOL=kitty|iterm2|none|auto`, and `PI_TRUE_COLOR=1|0|auto`. Explicit JSON booleans/protocols take precedence over those environment values. Use `"auto"` or omit a JSON value to leave environment and terminal detection in control.
 When `images.autoResize` is enabled, Atomic normalizes images before sending them to the model. Tool-result images are normalized after `tool_result` extension handlers run, so images an extension inserts receive the same limit; if processing fails, Atomic keeps the original image. Set it to `false` to preserve source dimensions.
 
 ### Shell
@@ -346,7 +352,7 @@ On Windows, select `powershell` instead of `bash`, or include both:
 }
 ```
 
-An empty array starts with no built-in tools while preserving extension and custom tools. `--tools` replaces this behavior with a strict allowlist covering all tools, `--no-tools` disables all tools, and `--no-builtin-tools` disables only the built-in defaults. `--exclude-tools` filters the resulting list. A project `defaultTools` array replaces the global array.
+An empty array starts with no built-in tools while preserving extension and custom tools. `--tools` replaces this behavior with a strict allowlist covering every non-mandatory tool, `--no-tools` disables every tool except mandatory ordinary `intercom`, and `--no-builtin-tools` disables only the built-in defaults. `--exclude-tools` filters the resulting list but cannot remove Intercom. A project `defaultTools` array replaces the global array.
 
 ### Sessions
 
@@ -385,7 +391,7 @@ When multiple sources specify a session directory, precedence is `--session-dir`
 
 Mermaid code blocks render as themed Unicode diagrams in interactive transcripts when they fit the available width. `"off"` keeps the Markdown fence, `"final"` renders only finalized responses, and `"streaming"` also renders partial assistant responses. Invalid or too-wide diagrams remain as code, and rendering is display-only: stored messages and model context keep the original Markdown. LaTeX rendering is also display-only and converts supported expressions to terminal-friendly Unicode math; set `markdown.latex` to `false` to keep the source form.
 
-The installed pi-tui 0.84.3 LaTeX renderer also handles whitespace and matrix layouts correctly.
+The installed pi-tui 0.84.4 LaTeX renderer also handles whitespace and matrix layouts correctly.
 
 ### Resources
 

package/docs/subagents.md

@@ -128,7 +128,7 @@ Status and interrupt use the live Rust registry and status watch; `list` and `ge
 
 Inside workflow stages, completion delivery observes the stage generation boundary. A completion received before the boundary closes is queued through the stage AgentSession and processed before the stage publishes its terminal snapshot. A completion that arrives after close is routed once to the parent/main chat and cannot reopen or append to the completed stage transcript. Explicit post-mortem stage chat is still available separately.
 
-Live progress and completed results show each step's resolved model, effective reasoning level, and applied fast-mode marker, including after a model fallback; parallel steps keep their metadata separate.
+Live progress and completed results show each step's resolved model, effective reasoning level, and applied fast-mode marker, including after a model fallback; parallel steps keep their metadata separate. Main-chat children use the launching chat's `codexFastMode.chat` setting, while children launched from a workflow stage (including a stage in a nested workflow) use `codexFastMode.workflow`. Eligible OpenAI children and Codex-transport aliases send `service_tier: priority`. A GitHub Copilot child is eligible only when its OAuth account catalog advertises the exact fast sibling; its outgoing request uses the `<model-id>-fast` wire model and its base-model label gets a separate `fast` marker. When the applicable scope is off or fallback selects an ineligible model, the request and label both return to the normal model without that marker.
 
 ## Orchestrator model and group policy
 
@@ -149,7 +149,7 @@ For adversarial review or research, prefer fresh context so the specialist inspe
 
 For parallel implementation work, `worktree: true` can give each child an isolated git worktree so concurrent edits do not clobber each other.
 
-Fresh child sessions use normal Atomic package discovery when an agent omits `extensions`, so bundled lightweight MCP, web-access, and Intercom wrappers are available just as they are in the parent. An explicit `extensions` field (including an empty list) intentionally switches the child to extension-allowlist mode and excludes unlisted builtins; it does not inherit the parent's normal discovery set.
+Fresh child sessions use normal Atomic package discovery when an agent omits `extensions`, so bundled lightweight MCP and web-access wrappers are available just as they are in the parent. An explicit `extensions` field, including an empty list, switches optional extensions to allowlist mode and excludes unlisted optional builtins; mandatory bundled Intercom remains loaded. The child does not inherit the parent's normal optional discovery set.
 
 Top-level parallel calls support up to 50 subagents after expanding each task's optional `count`. The extension's `parallel.maxTasks` setting defaults to 50 and can enforce a lower task limit; `parallel.concurrency` independently controls how many of those children run at once, while the Rust turn limiter admits at most four running turns per parent.
 

package/docs/usage.md

@@ -32,6 +32,7 @@ While ordinary agent work is active, the exact one-cell `∀` remains visible an
 | Shell command | `!command` runs and sends output to the model |
 | Hidden shell command | `!!command` runs without sending output to the model |
 | External editor | CTRL+G opens `$VISUAL` or `$EDITOR` |
+| Copy selection/message | Ctrl+X copies a retained fullscreen selection when `fullscreenCopyOnSelect` is disabled; otherwise it copies the last assistant message |
 
 See [Keybindings](/keybindings) for all shortcuts and customization.
 
@@ -231,7 +232,7 @@ For raw credential exports, stdout is empty on every non-zero exit but one. Once
 | `--mode rpc` | RPC mode over stdin/stdout; see [RPC mode](/rpc) |
 | `--export <in> [out]` | Export a session to HTML |
 
-Interactive sessions always use fullscreen: the transcript scrolls independently above a sticky dock containing the editor, status line, usage meter, extension widgets, and footer. Wheel and trackpad gestures go first to a focused workflow graph or stage chat overlay; events those overlays do not consume fall through to the alternate-screen viewport. Non-overlay focused components do not block pi-tui's mouse path, so transcript scrolling, scrollbar interaction, and drag selection still work. The `fullscreenExitOutput` setting controls what exiting prints: `"transcript"` (the default) paints the final transcript plus a session resume hint on the main screen, while `"resume-hint"` restores the previous screen and prints only the resume hint. See [Settings](/settings) and [Terminal setup](/terminal-setup).
+Interactive sessions always use fullscreen: the transcript scrolls independently above a sticky dock containing the editor, status line, usage meter, extension widgets, and footer. Wheel and trackpad gestures go first to a focused workflow graph or stage chat overlay; events those overlays do not consume fall through to the alternate-screen viewport. Non-overlay focused components do not block pi-tui's mouse path, so transcript scrolling, scrollbar interaction, and drag selection still work. Selection copies automatically by default; disable `fullscreenCopyOnSelect` to retain it for Ctrl+X. Ctrl+X closes workflow tool detail to the graph, clears a scoped-model selection, returns stage chat to its graph, or returns a workflow graph to main chat before the main editor may copy. `/copy` always copies the last assistant message. The `fullscreenExitOutput` setting controls what exiting prints: `"transcript"` (the default) paints the final transcript plus a session resume hint on the main screen, while `"resume-hint"` restores the previous screen and prints only the resume hint. See [Settings](/settings) and [Terminal setup](/terminal-setup).
 
 In print mode, Atomic also reads piped stdin and merges it into the initial prompt:
 
@@ -269,12 +270,12 @@ When a print-mode turn correctly finishes by calling an opt-in terminating struc
 
 | Option | Description |
 |--------|-------------|
-| `--tools <list>`, `-t <list>` | Allowlist specific built-in, extension, and custom tools |
-| `--exclude-tools <list>`, `-xt <list>` | Denylist specific built-in, extension, and custom tools |
+| `--tools <list>`, `-t <list>` | Allowlist specific built-in, extension, and custom tools; mandatory `intercom` remains available |
+| `--exclude-tools <list>`, `-xt <list>` | Denylist specific built-in, extension, and custom tools; mandatory `intercom` cannot be excluded |
 | `--no-builtin-tools`, `-nbt` | Disable built-in tools but keep extension/custom tools enabled |
-| `--no-tools`, `-nt` | Disable all tools |
+| `--no-tools`, `-nt` | Disable every tool except mandatory `intercom` |
 
-Default built-in tools: `read`, `bash`, `edit`, `write`, `find`, `search`, `ask_user_question`, `todo`, plus `powershell` on native Windows when a PowerShell executable is available. `find.paths` accepts directories, files, or glob paths such as `*.ts` and honors `timeout`; `search` accepts `pattern`, optional `paths`, `i`, `gitignore`, and `skip` for regex content-search pagination. Use `--exclude-tools` to disable one or more tools while leaving the rest available, for example `atomic --exclude-tools ask_user_question`. The `defaultTools` setting selects which built-in tools a session starts with; `--tools` replaces that default with a strict allowlist over built-in, custom, and extension tools; `--no-builtin-tools` removes only built-ins; `--no-tools` removes all tools. `ls` remains available as an SDK compatibility tool but is not enabled by default.
+Default built-in tools: `read`, `bash`, `edit`, `write`, `find`, `search`, `ask_user_question`, `todo`, plus `powershell` on native Windows when a PowerShell executable is available. `find.paths` accepts directories, files, or glob paths such as `*.ts` and honors `timeout`; `search` accepts `pattern`, optional `paths`, `i`, `gitignore`, and `skip` for regex content-search pagination. Use `--exclude-tools` to disable one or more non-mandatory tools while leaving the rest available, for example `atomic --exclude-tools ask_user_question`. The `defaultTools` setting selects which built-in tools a session starts with; `--tools` replaces that default with a strict allowlist over non-mandatory built-in, custom, and extension tools; `--no-builtin-tools` removes only built-ins; `--no-tools` removes every tool except ordinary bundled `intercom`. `ls` remains available as an SDK compatibility tool but is not enabled by default.
 
 ### Project Trust Options
 
@@ -290,7 +291,7 @@ Project trust gates `.atomic`/legacy `.pi` project resources, project package se
 | Option | Description |
 |--------|-------------|
 | `-e`, `--extension <source>` | Load an extension from path, npm, or git; repeatable |
-| `--no-extensions`, `-ne` | Disable extension discovery |
+| `--no-extensions`, `-ne` | Disable optional extension discovery; mandatory bundled Intercom remains loaded |
 | `--skill <path>` | Load a skill; repeatable |
 | `--no-skills`, `-ns` | Disable skill discovery |
 | `--prompt-template <path>` | Load a prompt template; repeatable |

package/docs/workflows.md

@@ -1571,7 +1571,7 @@ Pick and document one policy before the run:
 
 Use `block` for risky public contracts, data changes, security behavior, releases, or publication. `warn` is a practical default when a boundary review can replace live steering. Never degrade silently from `block` to `warn` or from guarded execution to `off`.
 
-Intercom capability is tool-gated. A stage with `noTools: "all"`, a `tools` allowlist that omits `intercom`, or `excludedTools: ["intercom"]` cannot use live steering. Use a boundary task or the selected fallback policy for that stage.
+Ordinary `intercom` is mandatory in every workflow model stage. `noTools: "all"`, restrictive `tools` allowlists, and `excludedTools` continue to restrict every other tool but cannot remove Intercom, so live steering remains available.
 
 ### Lifecycle, topology, and context rules
 
@@ -2425,7 +2425,7 @@ Sets the stage session's [Intercom](/intercom) home group. Every top-level workf
 
 `group` is accepted on `stage`/`task` options, on `ctx.parallel(...)` options, and per parallel step. Explicit values override the workflow invocation group; a step-level value also overrides its parallel-set value. A named string joins that group, including `group: "default"` to opt into the shared default group. Boolean `true` auto-generates one shared UUID group **per `ctx.parallel(...)` set** (minted once for every item in that set), while `true` on a non-parallel stage creates a fresh stage-only group. The trimmed, case-insensitive string sentinels `"true"` and `"auto"` have the same automatic behavior and are reserved.
 
-The full precedence is: explicit stage/task/parallel group > workflow invocation group > `ATOMIC_INTERCOM_GROUP` (or legacy `PI_INTERCOM_GROUP`) > Intercom config > `"default"`. Group assignment is **capability-gated**: a stage with `noTools: "all"`, a `tools` allowlist that omits `intercom`, or `excludedTools` containing `intercom` receives no group. `noTools: "builtin"` still keeps extension tools such as Intercom, so those stages inherit the workflow group unless they exclude Intercom. Subagents inherit their launching stage's resolved group by default (see [subagents.md](/subagents)). The subagent-only `contact_supervisor` channel keeps its broker-authorized cross-group route; ordinary client sends remain group-bound.
+The full precedence is: explicit stage/task/parallel group > workflow invocation group > `ATOMIC_INTERCOM_GROUP` (or legacy `PI_INTERCOM_GROUP`) > Intercom config > `"default"`. Every workflow model stage receives its workflow invocation group because ordinary Intercom is mandatory. Tool restrictions do not suppress that group; explicit `group` values retain their existing precedence. Subagents inherit their launching stage's resolved group by default (see [subagents.md](/subagents)). The subagent-only `contact_supervisor` channel keeps its broker-authorized cross-group route; ordinary client sends remain group-bound.
 
 Authors do not need to generate or pass a group through ordinary stages, tasks, parallel steps, nested workflows, or delegated subagents. Use an explicit named group or `group: true` only to create an intentional subgroup, such as isolating one reviewer level from another.
 
@@ -2489,7 +2489,7 @@ readonly noTools?: "all" | "builtin";
 readonly excludedTools?: readonly string[];
 ```
 
-`tools` is an allowlist across built-in and bundled extension tools; list every tool the stage should see. `excludedTools` and `noTools: "all"` still win.
+`tools` is an allowlist across built-in and bundled extension tools. `excludedTools` and `noTools: "all"` still win for every tool except mandatory ordinary `intercom`, which remains registered and active.
 
 The bundled `subagent` tool is available by default on the same terms as main chat. A workflow stage is a top-level session, so it may delegate once; the children it launches may not delegate or control another child. Delegation is exactly one level deep and nothing configures it — there is no config option, agent frontmatter field, or tool parameter for the level. The in-process admission door carries each child's issued depth in its typed child policy, the executor refuses any launch or `interrupt` from a session that was itself admitted as a child, and the Rust `SubagentControl` admission door refuses a child deeper than the single permitted level. That depth is never carried through process environment. Bundled subagent definitions from `@bastani/subagents` are available to that tool. Explicitly list tools such as `subagent`, `web_search`, `fetch_content`, or `intercom` when using an allowlist; in-process child sessions load the bundled resources while suppressing the workflow extension lifecycle.
 
@@ -3341,6 +3341,8 @@ If embedded provisioning fails without leaving retained-process cleanup pending,
 
 **Multiple concurrent Atomic sessions.** Every Atomic process launches DBOS with a unique executor id, and running root workflows carry owner/heartbeat metadata. Once an active model stage has a session path, Atomic records that identity after the stage-start record and awaits the checkpoint before the first model use, then runs serialized, unref'd liveness checkpoints on a bounded 30-second cadence for the root and nested scoped workflows. Each accepted checkpoint refreshes root metadata; timers stop on every stage exit and cannot keep Atomic alive. A persistent checkpoint fault fails the active stage instead of disappearing in a detached timer. A stage that is shutting down drains the checkpoint still in flight rather than abandoning it, so a failure that lands after the model turn finished is reported instead of discarded, and a stage whose final durability checkpoint fails is recorded as `failed` rather than `completed` — its caller receives the error and its concurrency slot is released either way. **Running workflows are never resume targets**: a running row with a fresh heartbeat is hidden from every session's picker and refused by direct `/workflow resume <id>` — resuming a workflow that is executing elsewhere would double-dispatch it. Once the heartbeat goes stale (about two minutes after a crash), an exact inspection or the resume picker reports the workflow as `crashed`.
 
+Within one Atomic process, DBOS writes stay ordered per durable root workflow. A slow or stalled write for one root does not block an independent top-level workflow from persisting its registration, reaching startup admission, or recording later checkpoints. Nested workflows share their durable root's write order. Process shutdown and explicit lifecycle drains still wait for every root.
+
 When two sessions race to resume the same paused workflow, a durable first-writer-wins claim decides exactly one winner; the loser reconciles to the authoritative state and reports that the workflow changed while resume was pending.
 
 ### How it works
@@ -3567,6 +3569,8 @@ Reload builds a complete replacement registry before publishing it. Concurrent r
 
 The top-level `/reload` command replaces the extension generation as well as rediscovering resources. Within the same Atomic process, the replacement workflows extension adopts the current session's run store and control registries before installing its UI, then remounts the below-editor panel from the adopted snapshot. In-process subagent children keep bundled workflow definitions as resources but do not load the workflows extension or expose its tool, so a child cannot rebind the parent's store. If an older extension generation already displaced a live run into an auxiliary session scope, `/reload` reclaims that live store together with its stage, job, cancellation, tool-control, and prompt owners; retained terminal history from the parent scope is merged before the panel remounts. Newly created session scopes never inherit another session's state. Installed builds can evaluate the extension and host SDK through separate jiti module copies; Atomic canonicalizes each generation's `pi.events` facade through a process-shared session-bus map so both copies adopt the same owners. In-flight `ctx.tool` callbacks and their durable node controls remain owned by that live run and may settle normally after reload; completed siblings remain checkpointed. A run or active tool node can also arrive after the UI is installed through durability hydration, which invalidates the store and mounts or updates the panel immediately. This same-process handoff differs from a process crash: after a real process exit there is no live callback to preserve, so explicit `/workflow resume` replays checkpoints and re-executes only unfinished tool work.
 
+After `/reload` invalidates the predecessor extension API, in-flight runs keep executing on that generation's module graph. Transcript appends from the captured persistence port are advisory: a stale-extension-context error is ignored so the run can complete, and any other persistence error still fails the run.
+
 The `/workflow` argument-completion popup reads that same live registry. Project, user, package-provided, and built-in workflow names therefore appear immediately after reload both after `/workflow ` and after `/workflow inputs `; restarting Atomic is not required.
 
 A successful rescan may still contain per-resource diagnostics. Both reload surfaces show `CONFIG_INVALID`, `IMPORT_FAILED`, `INVALID_DEFINITION`, `PATH_NOT_FOUND`, and duplicate-name diagnostics instead of reporting bare success while silently skipping a resource. Valid sibling workflows remain available. Fix the reported source/path and reload again; no process restart is required.
@@ -3739,9 +3743,9 @@ Workflow stage sessions inherit the same package and temporary `-e` resource dis
 
 ## Programmatic usage
 
-`@bastani/atomic/workflows` is Atomic's published workflow SDK. Import `workflow` from that specifier, import `Type` from `typebox`, and export the definition returned by `workflow({...})`. Keep runtime helpers such as widget factories and shared utilities in a subdirectory outside the top-level discovery scan, such as `.atomic/workflows/lib/`; see [Workflow Locations](#workflow-locations).
+`@bastani/atomic/workflows` is Atomic's published workflow SDK. Import `workflow` from that specifier, import `Type` from `typebox`, and export the definition returned by `workflow({...})`. Workflow helpers may also import the host TypeBox runtime subpaths `typebox/compile` and `typebox/value`; the legacy `@sinclair/typebox` root and matching subpaths remain supported. Keep runtime helpers such as widget factories and shared utilities in a subdirectory outside the top-level discovery scan, such as `.atomic/workflows/lib/`; see [Workflow Locations](#workflow-locations).
 
-Package authors list both `@bastani/atomic` and `typebox` in `peerDependencies`. The `@bastani/atomic` package publishes compiled JavaScript and declarations for `@bastani/atomic/workflows`, `@bastani/atomic/workflows/builtin`, and each `@bastani/atomic/workflows/builtin/*` module. TypeScript resolves those exports directly under `moduleResolution: NodeNext`. When Atomic executes a workflow file, its runtime loader resolves the same published specifiers to Atomic's in-memory SDK.
+Package authors list both `@bastani/atomic` and `typebox` in `peerDependencies`. The `@bastani/atomic` package publishes compiled JavaScript and declarations for `@bastani/atomic/workflows`, `@bastani/atomic/workflows/builtin`, and each `@bastani/atomic/workflows/builtin/*` module. TypeScript resolves those exports directly under `moduleResolution: NodeNext`. When Atomic executes a workflow file or an imported helper, its runtime loader resolves the workflow SDK and supported TypeBox aliases to the same in-memory host modules. It intentionally does not expose extension-only host modules such as the agent core, UI, provider transport, or lockfile implementation.
 
 ```ts
 import { workflow } from "@bastani/atomic/workflows";
@@ -4046,11 +4050,11 @@ Workflow stages can use faster inference on supported OpenAI and GitHub Copilot
 
 ### Fast mode
 
-Use `/fast` to manage fast mode separately for normal chat and workflow-stage sessions. The settings are `codexFastMode.chat` and `codexFastMode.workflow`; workflow stages use the workflow scope, not the chat scope. A stage inside a nested `ctx.workflow(...)` call keeps that workflow scope, and subagents launched by the stage inherit it.
+Use `/fast` to manage fast mode separately for normal chat and workflow-stage sessions. The settings are `codexFastMode.chat` and `codexFastMode.workflow`; main-chat subagents use the chat scope, while workflow stages use the workflow scope. A stage inside a nested `ctx.workflow(...)` call keeps that workflow scope, and subagents launched by the stage inherit it.
 
 Fast mode is eligible for supported `openai/*` and `openai-codex/*` providers, provider aliases that use the shared `openai-codex-responses` transport, and GitHub Copilot models whose OAuth account catalog advertises a fast variant. OpenAI requests use the priority service tier. GitHub Copilot requests use the account-supported fast variant without adding the OpenAI service-tier field. Azure OpenAI, OpenRouter, and generic OpenAI-compatible providers are not eligible.
 
-Atomic resolves eligibility for the effective model on every fallback attempt. A supported fallback can use fast mode even when the primary failed, while an unsupported fallback keeps its normal request behavior. Workflow stage model labels and stage-launched subagent result labels keep the raw model ID and append a separate `fast` marker; graph node cards keep their dependency metadata focused on topology and do not repeat that marker.
+Atomic resolves eligibility for the effective model on every fallback attempt. A supported fallback can use fast mode even when the primary failed, while an unsupported fallback keeps its normal request behavior. Workflow stage model labels and all subagent result labels keep the raw model ID and append a separate `fast` marker; for an entitled Copilot child, the marker appears exactly when the request uses the account-advertised `<model-id>-fast` variant. Graph node cards keep their dependency metadata focused on topology and do not repeat that marker.
 
 Enable workflow fast mode deliberately for broad workflows. Parallel fan-out and fallback attempts can multiply fast provider requests and usage.
 

package/npm-shrinkwrap.json

@@ -1,21 +1,21 @@
 {
 	"name": "@bastani/atomic",
-	"version": "0.9.16-alpha.8",
+	"version": "0.9.16",
 	"lockfileVersion": 3,
 	"requires": true,
 	"packages": {
 		"": {
 			"name": "@bastani/atomic",
-			"version": "0.9.16-alpha.8",
+			"version": "0.9.16",
 			"license": "MIT",
 			"dependencies": {
-				"@bastani/atomic-natives": "0.9.16-alpha.8",
+				"@bastani/atomic-natives": "0.9.16",
+				"@bastani/pi-ai": "0.9.16",
 				"@dbos-inc/dbos-sdk": "4.25.14",
-				"@earendil-works/pi-agent-core": "^0.84.3",
-				"@bastani/pi-ai": "0.9.16-alpha.8",
-				"@earendil-works/pi-client": "^0.84.3",
-				"@earendil-works/pi-protocol": "^0.84.3",
-				"@earendil-works/pi-tui": "^0.84.3",
+				"@earendil-works/pi-agent-core": "^0.84.4",
+				"@earendil-works/pi-client": "^0.84.4",
+				"@earendil-works/pi-protocol": "^0.84.4",
+				"@earendil-works/pi-tui": "^0.84.4",
 				"@modelcontextprotocol/ext-apps": "^1.7.5",
 				"@modelcontextprotocol/sdk": "^1.30.0",
 				"@mozilla/readability": "^0.6.0",
@@ -517,18 +517,18 @@
 			}
 		},
 		"node_modules/@bastani/atomic-natives": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives/-/atomic-natives-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives/-/atomic-natives-0.9.16.tgz",
 			"license": "MIT",
 			"optionalDependencies": {
-				"@bastani/atomic-natives-darwin-arm64": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-darwin-x64": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-linux-arm64-gnu": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-linux-arm64-musl": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-linux-x64-gnu": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-linux-x64-musl": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-win32-arm64-msvc": "0.9.16-alpha.8",
-				"@bastani/atomic-natives-win32-x64-msvc": "0.9.16-alpha.8"
+				"@bastani/atomic-natives-darwin-arm64": "0.9.16",
+				"@bastani/atomic-natives-darwin-x64": "0.9.16",
+				"@bastani/atomic-natives-linux-arm64-gnu": "0.9.16",
+				"@bastani/atomic-natives-linux-arm64-musl": "0.9.16",
+				"@bastani/atomic-natives-linux-x64-gnu": "0.9.16",
+				"@bastani/atomic-natives-linux-x64-musl": "0.9.16",
+				"@bastani/atomic-natives-win32-arm64-msvc": "0.9.16",
+				"@bastani/atomic-natives-win32-x64-msvc": "0.9.16"
 			},
 			"engines": {
 				"bun": ">=1.4.0",
@@ -536,8 +536,8 @@
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-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-arm64/-/atomic-natives-darwin-arm64-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-arm64/-/atomic-natives-darwin-arm64-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"darwin"
@@ -548,8 +548,8 @@
 			"optional": true
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 		"node_modules/@bastani/atomic-natives-darwin-x64": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-x64/-/atomic-natives-darwin-x64-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-x64/-/atomic-natives-darwin-x64-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"darwin"
@@ -560,8 +560,8 @@
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 		"node_modules/@bastani/atomic-natives-linux-arm64-gnu": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-gnu/-/atomic-natives-linux-arm64-gnu-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-gnu/-/atomic-natives-linux-arm64-gnu-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -575,8 +575,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-arm64-musl": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-musl/-/atomic-natives-linux-arm64-musl-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-musl/-/atomic-natives-linux-arm64-musl-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -590,8 +590,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-x64-gnu": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-gnu/-/atomic-natives-linux-x64-gnu-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-gnu/-/atomic-natives-linux-x64-gnu-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
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@@ -605,8 +605,8 @@
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 		},
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-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-musl/-/atomic-natives-linux-x64-musl-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-musl/-/atomic-natives-linux-x64-musl-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -620,8 +620,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-win32-arm64-msvc": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-arm64-msvc/-/atomic-natives-win32-arm64-msvc-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-arm64-msvc/-/atomic-natives-win32-arm64-msvc-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"win32"
@@ -632,8 +632,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-win32-x64-msvc": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-x64-msvc/-/atomic-natives-win32-x64-msvc-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-x64-msvc/-/atomic-natives-win32-x64-msvc-0.9.16.tgz",
 			"license": "MIT",
 			"os": [
 				"win32"
@@ -644,13 +644,13 @@
 			"optional": true
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 		"node_modules/@bastani/pi-ai": {
-			"version": "0.9.16-alpha.8",
-			"resolved": "https://registry.npmjs.org/@bastani/pi-ai/-/pi-ai-0.9.16-alpha.8.tgz",
+			"version": "0.9.16",
+			"resolved": "https://registry.npmjs.org/@bastani/pi-ai/-/pi-ai-0.9.16.tgz",
 			"license": "MIT",
 			"dependencies": {
 				"@anthropic-ai/sdk": "0.91.1",
 				"@aws-sdk/client-bedrock-runtime": "3.1048.0",
-				"@earendil-works/pi-telemetry": "0.84.2",
+				"@earendil-works/pi-telemetry": "0.84.4",
 				"@google/genai": "1.52.0",
 				"@smithy/node-http-handler": "4.7.3",
 				"http-proxy-agent": "7.0.2",
@@ -701,13 +701,13 @@
 			]
 		},
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-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-agent-core/-/pi-agent-core-0.84.3.tgz",
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+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-agent-core/-/pi-agent-core-0.84.4.tgz",
+			"integrity": "sha512-HyUnjaOXj6oN/6SNcr8A1J/ElRQA50FtIE0XUTSKAQVqmdlb9qdojOyUQwF/jULE5+yOEtGuVgi/N1RnBiNG+g==",
 			"license": "MIT",
 			"dependencies": {
-				"@earendil-works/pi-ai": "^0.84.3",
-				"@earendil-works/pi-telemetry": "^0.84.3",
+				"@earendil-works/pi-ai": "^0.84.4",
+				"@earendil-works/pi-telemetry": "^0.84.4",
 				"diff": "8.0.4",
 				"ignore": "7.0.5",
 				"typebox": "1.3.7",
@@ -717,24 +717,15 @@
 				"node": ">=22.19.0"
 			}
 		},
-		"node_modules/@earendil-works/pi-agent-core/node_modules/@earendil-works/pi-telemetry": {
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-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-telemetry/-/pi-telemetry-0.84.3.tgz",
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-			"license": "MIT",
-			"engines": {
-				"node": ">=22.19.0"
-			}
-		},
 		"node_modules/@earendil-works/pi-ai": {
-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-ai/-/pi-ai-0.84.3.tgz",
-			"integrity": "sha512-M0YUV8vNO3y2WwWSyY8ijKJV5W4gkSUixuvk+Z00ZBjsyMfsdXfITsHEwP1UIf09YRWXT6oGn0GlCamt+P32XQ==",
+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-ai/-/pi-ai-0.84.4.tgz",
+			"integrity": "sha512-AClAZxf5+c4RRu44NJPS6wyQy+Nmq+Mzyyrdvm4ZVMNuixelO02RZX4G4Aq1F145Yzp43wnM5S+hLlSI7ypfVw==",
 			"license": "MIT",
 			"dependencies": {
 				"@anthropic-ai/sdk": "0.91.1",
 				"@aws-sdk/client-bedrock-runtime": "3.1048.0",
-				"@earendil-works/pi-telemetry": "^0.84.3",
+				"@earendil-works/pi-telemetry": "^0.84.4",
 				"@google/genai": "1.52.0",
 				"@smithy/node-http-handler": "4.7.3",
 				"http-proxy-agent": "7.0.2",
@@ -750,31 +741,22 @@
 				"node": ">=22.19.0"
 			}
 		},
-		"node_modules/@earendil-works/pi-ai/node_modules/@earendil-works/pi-telemetry": {
-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-telemetry/-/pi-telemetry-0.84.3.tgz",
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-			"license": "MIT",
-			"engines": {
-				"node": ">=22.19.0"
-			}
-		},
 		"node_modules/@earendil-works/pi-client": {
-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-client/-/pi-client-0.84.3.tgz",
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+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-client/-/pi-client-0.84.4.tgz",
+			"integrity": "sha512-q398WY/3ZQHTizk7IKxApzqFV0xt4yM9LkSkwyqeLK5Bj5RwRjOWxESt26z4LgNp4O+8hqhqFPf/8fj4H5rE4A==",
 			"license": "MIT",
 			"dependencies": {
-				"@earendil-works/pi-protocol": "^0.84.3"
+				"@earendil-works/pi-protocol": "^0.84.4"
 			},
 			"engines": {
 				"node": ">=22.19.0"
 			}
 		},
 		"node_modules/@earendil-works/pi-protocol": {
-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-protocol/-/pi-protocol-0.84.3.tgz",
-			"integrity": "sha512-9a4g6WhLOvRqvsIOFaWxg/2gdrbY4Thclwj5ipLUPAWChfsDJ/8XdPc2sRhSOkD6EsxpEFJz3xppcfwI6EcZDg==",
+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-protocol/-/pi-protocol-0.84.4.tgz",
+			"integrity": "sha512-acyE9ozxkMiWiz/xyWpU0O9vwnYv0hyG889Vniv6Sg9c9zfsX+8MePnDNphBacY2Fvm1rxdsGmiVDSZl9yuDFA==",
 			"license": "MIT",
 			"dependencies": {
 				"typebox": "1.3.7"
@@ -784,18 +766,18 @@
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 		"node_modules/@earendil-works/pi-telemetry": {
-			"version": "0.84.2",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-telemetry/-/pi-telemetry-0.84.2.tgz",
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+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-telemetry/-/pi-telemetry-0.84.4.tgz",
+			"integrity": "sha512-8e2CuxM+ht+hedQXTZmi5JVl6/xDK9RpSDL2+MbITevKYQhMZ/z6lJOTFgox3HQyGxO8mOZEtYGVeQNaD4OzqA==",
 			"license": "MIT",
 			"engines": {
 				"node": ">=22.19.0"
 			}
 		},
 		"node_modules/@earendil-works/pi-tui": {
-			"version": "0.84.3",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-tui/-/pi-tui-0.84.3.tgz",
-			"integrity": "sha512-fS6OEQKEEALnKa6Uw8LcgZZ+9CWck7f3MQSCETQp6leUgIFwMEDtKmOUnL9nsYm+RIPmy7OmplVxYRbV6hiaFg==",
+			"version": "0.84.4",
+			"resolved": "https://registry.npmjs.org/@earendil-works/pi-tui/-/pi-tui-0.84.4.tgz",
+			"integrity": "sha512-nPUnwDkLtupPXnZQYrCwPFcuTydCDqTY6ZbFqhsL4S4kVq0AT418kPa/6uXwtaCD+MjBNBltb7ScTYX65yeE1w==",
 			"license": "MIT",
 			"dependencies": {
 				"get-east-asian-width": "1.6.0",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.9.16-alpha.8",
+  "version": "0.9.16",
   "description": "Atomic coding agent CLI with read, bash, edit, write tools and session management",
   "type": "module",
   "atomicConfig": {
@@ -79,13 +79,13 @@
     "prepublishOnly": "bun run clean && bun run build && bun run shrinkwrap"
   },
   "dependencies": {
-    "@bastani/atomic-natives": "0.9.16-alpha.8",
+    "@bastani/atomic-natives": "0.9.16",
+    "@bastani/pi-ai": "0.9.16",
     "@dbos-inc/dbos-sdk": "4.25.14",
-    "@earendil-works/pi-agent-core": "^0.84.3",
-    "@bastani/pi-ai": "0.9.16-alpha.8",
-    "@earendil-works/pi-client": "^0.84.3",
-    "@earendil-works/pi-protocol": "^0.84.3",
-    "@earendil-works/pi-tui": "^0.84.3",
+    "@earendil-works/pi-agent-core": "^0.84.4",
+    "@earendil-works/pi-client": "^0.84.4",
+    "@earendil-works/pi-protocol": "^0.84.4",
+    "@earendil-works/pi-tui": "^0.84.4",
     "@modelcontextprotocol/ext-apps": "^1.7.5",
     "@modelcontextprotocol/sdk": "^1.30.0",
     "@mozilla/readability": "^0.6.0",