pi-subagents 0.62.0 → 0.63.0

package/CHANGELOG.md

@@ -3,6 +3,34 @@
 
 ## [Unreleased]
 
+## [0.63.0] - 2026-09-01
+
+### Highlights
+- Workflow progress is easier to scan in status, Fleet, and live widgets.
+- Additional agent folders can now be configured without copying definitions into one directory.
+- Worktrunk users get managed worktrees automatically, with native Git available as the fallback.
+- Fleet can jump straight into the selected child run's Herdr inspector.
+- Async runs clean up and report edge cases more reliably.
+
+### Added
+- Show workflow progress as stacked checklist summaries in status, Fleet, and live widget views (#1806).
+- Add configurable extra agent scan directories with one-segment wildcard expansion. Thanks to [@mystery4f](https://github.com/mystery4f) for #1801.
+- Make Worktrunk a first-class managed worktree provider, selected automatically when available with native Git as the fallback (#1800).
+- Let Fleet open the selected async child in its child-specific Herdr inspector. Thanks to [@stekman08](https://github.com/stekman08) for #1790.
+
+### Changed
+- Show workflow checklist phases first in collapsed views, while keeping child details available when expanded (#1810).
+
+### Fixed
+- Keep isolated test runs from writing agent definitions into an inherited `PI_CODING_AGENT_DIR`. Thanks to [@mapleluvr](https://github.com/mapleluvr) for #1809.
+- Prevent nested tool-availability diagnostics from failing an otherwise valid parent result. Thanks to [@robertvangor](https://github.com/robertvangor) for #1802.
+- Free async capacity correctly after workflows finish, even when saved step status is stale. Thanks to [@boggylp](https://github.com/boggylp) for #1804.
+- Make `subagents.agentOverrides.<name>` replace matching custom-agent frontmatter fields, consistently with builtin agents. Thanks to [@expoli](https://github.com/expoli) for #1796.
+- Strip the trailing Pi turn-timing footer from child output. Thanks to [@fkhawajagh](https://github.com/fkhawajagh) for #1792.
+- Keep inferred acceptance reports out of reviewer and read-only child prompts. Thanks to [@expoli](https://github.com/expoli) for #1797.
+- Preserve coordinated read-only intent when direct async children resume, and show captured structured output in completion and status evidence. Thanks to [@fkhawajagh](https://github.com/fkhawajagh) for #1788.
+- Keep macOS subagent tasks out of argv by delivering them through temporary files. Thanks to [@josephkallas](https://github.com/josephkallas) for #1793.
+
 ## [0.62.0] - 2026-08-31
 
 ### Highlights

package/docs/agents.md

@@ -27,6 +27,7 @@ Discovery notes:
 
 - Project discovery also reads legacy `.agents/**/*.md` files. If both `.agents/` and the project config agents directory define the same parsed runtime agent name, the project config directory wins.
 - Nested subdirectories are discovered recursively. `.chain.md` files do not define agents.
+- User and project settings can add extra recursive scan roots with `subagents.agentScanDirs`; fixed user/project agent directories keep higher priority than same-name agents from scan roots.
 - Installed Pi packages can expose agent directories from either `{"pi-subagents":{"agents":["./agents"]}}` or `{"pi":{"subagents":{"agents":["./agents"]}}}` in their package manifest. Package agents load above builtins and below user/project agents.
 - Use `agentScope: "user" | "project" | "both"` to control discovery. `both` is the default, and project definitions win runtime-name collisions.
 
@@ -189,9 +190,9 @@ The `researcher` builtin uses `web_search`, `fetch_content`, and `get_search_con
 pi install npm:pi-web-access
 ```
 
-## Overriding builtins
+## Overriding builtins and custom agents
 
-You can override selected builtin fields without copying the whole agent. Overrides live in settings:
+You can override selected agent fields without copying the whole agent. Overrides live in settings:
 
 - User: `~/.pi/agent/settings.json`
 - Project: project config settings file (`.pi/settings.json` in standard Pi)
@@ -213,9 +214,9 @@ Supported override fields: `description`, `output`, `outputMode`, `defaultReads`
 
 - `description` replaces the discovered description for builtin and custom agents, which lets list output show deployment-specific routing or model metadata.
 - Use `output: false`, `defaultReads: false`, `defaultContext: false`, or `acceptanceRole: false` to clear an inherited value.
-- Use `tools: "inherit"` on a builtin when that one role should omit its bundled tool allowlist and receive Pi's normal builtins and ambient extensions. This keeps strict tools as the default for other builtins.
+- Use `tools: "inherit"` when that one role should omit its bundled or frontmatter tool allowlist and receive Pi's normal builtins and ambient extensions.
 - Project overrides beat user overrides.
-- Matching user and project agents also receive override fields that their frontmatter leaves unset, so a shared project config agent can keep the persona while local settings choose the model.
+- Matching package, user, and project agents also receive override fields, which replace the same fields declared in their frontmatter. This lets a shared agent keep its persona while local settings choose the effective model, context, tools, or other supported options.
 
 Disable and restore:
 

package/docs/configuration.md

@@ -2,7 +2,7 @@
 
 `pi-subagents` reads optional JSON config from `~/.pi/agent/extensions/subagent/config.json`. This page lists every key, plus the environment variables and the settings-file keys that affect config resolution.
 
-Settings-level keys (`subagents.defaultModel`, `defaultProvider`, `defaultThinking`, `defaultExtensions`, `agentOverrides`, `modelScope`, `disableThinking`, `disableBuiltins`, watchdog settings) live in Pi settings files, not this config file. `modelScope.agents.<name>` adds per-agent restrictions, and `allow: ["inherit"]` permits the current parent model. See [models.md](models.md), [agents.md](agents.md), and [watchdog.md](watchdog.md).
+Settings-level keys (`subagents.defaultModel`, `defaultProvider`, `defaultThinking`, `defaultExtensions`, `agentOverrides`, `agentScanDirs`, `modelScope`, `disableThinking`, `disableBuiltins`, watchdog settings) live in Pi settings files, not this config file. `modelScope.agents.<name>` adds per-agent restrictions, and `allow: ["inherit"]` permits the current parent model. See [models.md](models.md), [agents.md](agents.md), and [watchdog.md](watchdog.md).
 
 ## Project root resolution (settings)
 
@@ -18,6 +18,20 @@ By default, project settings resolve from the nearest parent directory that cont
 
 `"git-root"` keeps package discovery, project agents, chains, and `agentOverrides` anchored to the git worktree root when that root also has Pi project config. A nested project can still opt back into nearest-root behavior by setting `"projectRootResolution": "nearest"` in its own `.pi/settings.json`.
 
+## Extra agent scan directories (settings)
+
+Add recursive user or project agent roots with `subagents.agentScanDirs` in Pi settings:
+
+```json
+{
+  "subagents": {
+    "agentScanDirs": ["~/.pi/flows/*/agents"]
+  }
+}
+```
+
+Entries support `~` expansion. A single `*` path segment expands one directory level, so package-like folders can each expose an `agents/` directory. Missing directories are ignored. Fixed user/project agent directories still win over same-name agents from scan roots.
+
 ## `modelExclusions`
 
 ```json
@@ -356,7 +370,7 @@ Overrides the command used to launch child Pi processes. Package wrappers can se
 export PI_SUBAGENT_TASK_DELIVERY=file   # auto | file (default: auto)
 ```
 
-Controls how the task text reaches the child Pi process. `auto` (default) passes short tasks as an inline argv token and writes tasks longer than 8000 characters to a temp `task.md` referenced as `@<path>`. `file` always uses a temp file, keeping the task out of argv entirely.
+Controls how the task text reaches the child Pi process. `auto` (default) passes short non-macOS tasks as an inline argv token, and writes macOS tasks plus tasks longer than 8000 characters to a temp `task.md` referenced as `@<path>`. `file` always uses a temp file, keeping the task out of argv entirely.
 
 Use `file` on hosts where endpoint protection (EDR) pre-execution scanning denies child processes whose command line embeds a long natural-language task — that denial surfaces as an immediate zero-activity `SIGKILL`. Independently of this setting, startup retries automatically escalate to file delivery after an unexplained zero-activity `SIGKILL`. Empty, whitespace-only, or unrecognized values fall back to `auto`.
 
@@ -392,6 +406,18 @@ The default injected guidance tells children to use `contact_supervisor` with `r
 
 Sets the base directory for `worktree: true` runs. Relative paths resolve from the repository root, `~/...` expands to your home directory, and `PI_SUBAGENTS_WORKTREE_DIR` is used when config is unset. The default remains the system temp directory.
 
+## `worktreeProvider`
+
+```json
+{ "worktreeProvider": "auto", "worktreeBranchPrefix": "pi-subagents/" }
+```
+
+Selects the managed worktree allocator: `auto` (the default) uses Worktrunk when its machine-readable interface is available and otherwise falls back to Pi's native Git worktrees; `native` always uses Pi's Git implementation; and `worktrunk` fails closed when Worktrunk is unavailable or incompatible. A configured `worktreeBaseDir` (or `PI_SUBAGENTS_WORKTREE_DIR`) selects native allocation and cannot be combined with explicit `worktrunk`.
+
+`worktreeBranchPrefix` is normalized as a Git ref namespace and defaults to `pi-subagents/`. Branch names include readable task/lane identity plus run and fan-out indexes. Pi continues to own setup hooks, launch, handoff/diff evidence, resume, and cleanup; Worktrunk is used only to allocate and report the worktree path.
+
+Set `worktree` to `true` to make managed worktree isolation the default for launches that omit the per-call `worktree` flag. A per-call value still takes precedence.
+
 ## `worktreeSetupHook`
 
 ```json

package/docs/models.md

@@ -11,7 +11,7 @@ Builtin agents inherit your current Pi default model. This keeps new installs fr
 - `subagents.agentOverridesByProvider.<provider>.<name>` — layer role fields for the active parent provider.
 - Per-run overrides — for one launch only.
 
-Precedence, strongest first: per-run override → agent frontmatter `model` → provider-scoped role override → `agentOverrides.<name>.model` → `subagents.defaultModel` → the parent session model. A provider preference does not replace this order; it only resolves bare model ids when the active registry has more than one match. Fully qualified `provider/model` strings still win exactly.
+Precedence, strongest first: per-run override → provider-scoped role override → `agentOverrides.<name>.model` → agent frontmatter `model` → `subagents.defaultModel` → the parent session model. A provider preference does not replace this order; it only resolves bare model ids when the active registry has more than one match. Fully qualified `provider/model` strings still win exactly.
 
 Use `model: "inherit"` in agent frontmatter or `agentOverrides.<name>.model` to select the current parent session model explicitly.
 
@@ -81,7 +81,7 @@ For a persistent role override with a backup model for provider failures:
 }
 ```
 
-`subagents.defaultModel` and `subagents.defaultProvider` apply to builtin, package, user, and project agents. `defaultModel` fills only agents that do not set `model` in frontmatter. `defaultProvider` is also applied to frontmatter and override models so bare ids resolve against the intended provider. Per-run model overrides and `agentOverrides.<name>.model` still win, and explicit agent frontmatter still wins over the global default. The same `agentOverrides` block can change `tools`, `skills`, inherited context, prompt text, or disable a builtin (see [agents.md](agents.md)). Matching user and project agents also receive override fields that their frontmatter leaves unset, so a shared project config agent can keep the persona while local settings choose the model or provider.
+`subagents.defaultModel` and `subagents.defaultProvider` apply to builtin, package, user, and project agents. `defaultModel` fills only agents that do not set `model` in frontmatter. `defaultProvider` is also applied to frontmatter and override models so bare ids resolve against the intended provider. Per-run model overrides and `agentOverrides.<name>.model` win over frontmatter and the global default. The same `agentOverrides` block can change `tools`, `skills`, inherited context, prompt text, or disable an agent (see [agents.md](agents.md)); matching custom-agent frontmatter is replaced for any field set by the override.
 
 ## Fast mode
 
@@ -116,7 +116,7 @@ One interaction worth knowing for tier 4: forked context over an Anthropic paren
 
 ## Thinking level defaults
 
-Set `subagents.defaultThinking` to give builtin, package, user, and project agents without a `thinking` value a shared thinking level, independent of the parent session's default. Project settings win over user settings. Explicit frontmatter, `agentOverrides.<name>.thinking`, and per-run thinking overrides still win. `thinking: false` remains an explicit opt-out:
+Set `subagents.defaultThinking` to give builtin, package, user, and project agents without a `thinking` value a shared thinking level, independent of the parent session's default. Project settings win over user settings. Matching `agentOverrides.<name>.thinking` and per-run thinking overrides replace frontmatter; otherwise explicit frontmatter remains in effect. `thinking: false` remains an explicit opt-out:
 
 ```json
 {
@@ -129,7 +129,7 @@ Set `subagents.defaultThinking` to give builtin, package, user, and project agen
 }
 ```
 
-If your provider rejects model IDs with thinking suffixes, set `subagents.disableThinking: true` in user or project settings. That clears bundled builtin thinking defaults in one place. An explicit higher-precedence `agentOverrides.<name>.thinking` value can opt a role back in. Existing custom-agent frontmatter remains authoritative.
+If your provider rejects model IDs with thinking suffixes, set `subagents.disableThinking: true` in user or project settings. That clears bundled builtin thinking defaults in one place. An explicit higher-precedence `agentOverrides.<name>.thinking` value can opt a role back in or replace custom-agent frontmatter thinking.
 
 ### Thinking ceiling
 
@@ -154,7 +154,7 @@ Set `subagents.defaultExtensions` to give builtin, package, user, and project ag
 - Empty array: sets `extensions: []` for agents that do not explicitly define it, disabling ambient extension loading.
 - Non-empty array: supplies that allowlist to agents that do not explicitly define one.
 
-Project settings win over user settings. Use `agentOverrides.<name>.extensions` for per-agent settings; explicit custom-agent frontmatter remains authoritative.
+Project settings win over user settings. Use `agentOverrides.<name>.extensions` for per-agent settings; a matching override replaces custom-agent frontmatter for that field.
 
 ```json
 {

package/docs/observability.md

@@ -54,7 +54,7 @@ After you expand it:
     reviewer · running        38s · ↓ 1.1k window · 1.4k spent
 ```
 
-When the focused editor is empty, press `↓` or `←` to expand the summary into `main` plus active children with agent name, state, elapsed time, and token usage. When providers report usage, `window` is the latest assistant turn's input plus cache-read tokens, while `spent` keeps the cumulative input-plus-output total. Old run artifacts without window data keep the existing token-total label. The compact line counts active current-session work and Herdr project panes. Then use `↑`/`↓` or `j`/`k` to select a child and `Enter` to inspect it. Printable navigation keys are never intercepted before activation.
+When the focused editor is empty, press `↓` or `←` to expand the summary into `main` plus active children with agent name, state, elapsed time, and token usage. When providers report usage, `window` is the latest assistant turn's input plus cache-read tokens, while `spent` keeps the cumulative input-plus-output total. Old run artifacts without window data keep the existing token-total label. The compact line counts active current-session work and Herdr project panes. Then use `↑`/`↓` or `j`/`k` to select a child and `Enter` to open the Fleet lobby; press `Enter` or `H` there to open its child-specific Herdr inspector. Printable navigation keys are never intercepted before activation.
 
 FleetView replaces the legacy above-editor async widget by default. Successful background completions stay quiet so inactive Pi tabs are not marked unread, while failed or paused completions still notify the originating session. Parallel runs show every active child independently. Chains with parallel groups keep their grouped shape in progress and results, so failed or paused agents stay visible next to completed ones. When a child is explicitly allowed to fan out with `tools: subagent` or `allowNestedSubagents: true`, its nested runs appear under that parent child in the main status tree instead of being hidden inside the child process.
 
@@ -70,6 +70,7 @@ Default keys:
 - `x`/`Ctrl+O` — toggle tool details
 - `r` — refresh
 - `Esc` — close
+- `Enter` — open the selected inspectable async child in its child-specific Herdr inspector
 - `s` — compose an acknowledged message to a selected live async child; Tab cycles `steer`, `follow_up`, and `auto`
 - `D` — stop a selected child's top-level async run after confirmation
 - `H` — open the selected active async child in a Herdr inspector pane (Herdr 0.7.5+)
@@ -78,6 +79,8 @@ Set `fleetKeybindings` in the extension config to replace inspector-level keys w
 
 `Ctrl+Alt+F` opens the same inspector even while a foreground turn is active and slash input is queued.
 
+Enter and `H` use the existing Herdr pane path. In a child-specific Herdr inspector, type ordinary guidance and press Enter to send it through the acknowledged steer channel; `steer <message>`, `status`, and `stop` remain available as explicit controls.
+
 Without a TUI, `/subagents-fleet` retains the textual `subagent({ action: "status", view: "fleet" })` fallback, and mutations use explicit commands: run `/subagents-stop` and pick from the selector, or use `/subagents-stop <run-id>` / `subagent({ action: "stop", id: "..." })` when you already know the id.
 
 Use `/subagents-detach [run-id]` only for an active foreground single-subagent run you want to leave running without terminating; the eventual result remains available through status/wait.

package/docs/tool-reference.md

@@ -393,7 +393,7 @@ Acceptance evidence levels are `auto`, `none`, `attested`, `checked`, and `verif
 Review is a separate gate configured with `acceptance.review`:
 
 - Async, risky, and dynamic writer contexts infer checked evidence plus `review: { agent: "reviewer", required: true }`.
-- Read-only tasks infer lightweight attestation.
+- Reviewer/read-only calls infer no acceptance by default; explicit acceptance requests still apply.
 - Normal writer tasks infer checked evidence without review.
 
 Agent frontmatter or `subagents.agentOverrides` may set `acceptanceRole: "read-only" | "writer"` for ambiguous tasks. Explicit task mutation or no-edit intent wins over that role, while omitted metadata preserves the existing reviewer/scout/worker name heuristics. The role affects acceptance inference only and does not change tool access.
@@ -420,7 +420,7 @@ Acceptance provenance is stored separately from child prose. `evidenceStatus` pr
 
 ### The acceptance report
 
-For `attested` or stricter levels, the child prompt includes a standardized acceptance section and asks for a fenced `acceptance-report` JSON block. With `outputSchema`, set `acceptance.report: "on"` to require the same report in the final `structured_output` call, or `"off"` to keep the fenced-report path. Omitting `report` preserves the default behavior. Runs without `outputSchema` never gain a standalone structured-output tool from this option.
+For `attested` or stricter levels, the child prompt includes a standardized acceptance section and asks for a fenced `acceptance-report` JSON block. Reviewer/read-only inference resolves to `none`, so it does not add this section; explicit acceptance still does. With `outputSchema`, set `acceptance.report: "on"` to require the same report in the final `structured_output` call, or `"off"` to keep the fenced-report path. Omitting `report` preserves the default behavior. Runs without `outputSchema` never gain a standalone structured-output tool from this option.
 
 The parser canonicalizes known enum synonyms, snake_case report keys and wrappers, underscore fence tags, unambiguous scalar arrays, string booleans, and criterion-id separators. Unknown or ambiguous keys and enum values fail with field-level diagnostics. Explicit empty `changedFiles` and `testsAddedOrUpdated` arrays are recorded as not applicable; missing fields and empty required command or validation evidence still fail.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pi-subagents",
-  "version": "0.62.0",
+  "version": "0.63.0",
   "description": "Pi extension for single-agent delegation and scripted multi-agent workflows",
   "author": "Nico Bailon",
   "license": "MIT",

package/skills/pi-subagents/references/management-authoring-rpc.md

@@ -85,7 +85,7 @@ subagent({ action: "reset", agent: "reviewer" })
 Use management actions when the system needs to create or edit subagents on
 demand without dropping into raw file editing.
 
-Management actions create or update user/project agent files. `config.name` is the local frontmatter name; optional `config.package` registers and looks up the runtime name as `{package}.{name}`. Use the dotted runtime name for `get`, `update`, `delete`, slash commands, and scripted workflow steps. For small builtin changes such as a model swap, prefer `subagents.agentOverrides` in settings. Durable `.chain.md` definitions are legacy records, not a current authoring target; use `workflowScript` or `/prompt-workflow` for repeatable orchestration.
+Management actions create or update user/project agent files. `config.name` is the local frontmatter name; optional `config.package` registers and looks up the runtime name as `{package}.{name}`. Use the dotted runtime name for `get`, `update`, `delete`, slash commands, and scripted workflow steps. For small agent changes such as a model swap, prefer `subagents.agentOverrides` in settings. Durable `.chain.md` definitions are legacy records, not a current authoring target; use `workflowScript` or `/prompt-workflow` for repeatable orchestration.
 
 ## Creating and Editing Agents by File
 

package/skills/pi-subagents/references/prompting-and-roles.md

@@ -185,7 +185,7 @@ Builtin `worker` and `delegate` use strict tool allowlists and do not inherit am
 
 Builtin agents inherit the current Pi default model unless a run, user setting, project setting, or `subagents.defaultModel` overrides `model`. The table records recommended tier routing, not shipped hard defaults; explicit run, user, or project settings still win. Keep the parent/orchestrator on the ordinary strong default model unless parent/user policy says otherwise. Override builtin defaults before copying full agent files when a small tweak is enough.
 
-Set `subagents.defaultThinking` to apply a shared thinking level to builtin, package, user, and project agents whose frontmatter leaves `thinking` unset. Project settings win over user settings; explicit frontmatter (including `thinking: false`), `agentOverrides.<name>.thinking`, and per-run overrides remain more specific. This setting affects child agents only and does not change the parent session's default thinking level.
+Set `subagents.defaultThinking` to apply a shared thinking level to builtin, package, user, and project agents whose frontmatter leaves `thinking` unset. Project settings win over user settings; matching `agentOverrides.<name>.thinking` and per-run overrides replace frontmatter, while an explicit frontmatter value remains in effect when no matching override is set. This setting affects child agents only and does not change the parent session's default thinking level.
 
 ```json
 {
@@ -288,8 +288,8 @@ Use `fallbackModels` when a tier has provider quota or availability risk. Prefer
 If a provider rejects model IDs with thinking suffixes, use
 `subagents.disableThinking: true` in user or project settings to clear bundled
 builtin thinking defaults globally. A higher-precedence per-agent `thinking`
-override can opt one builtin back in. Existing custom-agent frontmatter remains authoritative.
+override can opt one builtin back in or replace custom-agent frontmatter thinking.
 
-Set `subagents.defaultExtensions` to give agents without an `extensions` field a shared child extension allowlist. Omit it to preserve ambient extension discovery, set it to `[]` to disable ambient extensions by default, or use `agentOverrides.<name>.extensions` for one agent. Explicit custom-agent frontmatter still wins.
+Set `subagents.defaultExtensions` to give agents without an `extensions` field a shared child extension allowlist. Omit it to preserve ambient extension discovery, set it to `[]` to disable ambient extensions by default, or use `agentOverrides.<name>.extensions` for one agent. A matching override replaces custom-agent frontmatter for that field.
 
 Tool description modes live in `~/.pi/agent/extensions/subagent/config.json`, not `subagents` settings. The default uses split prompt metadata: a short tool description plus active `promptSnippet` and `promptGuidelines`. Set `toolDescriptionMode` to `full` or `compact` to force one description string, or `custom` to read `subagent-tool-description.md` from the project config dir or agent dir; invalid custom files fall back to full mode and the safety guidance is still appended.

package/src/agents/agent-management.ts

@@ -250,13 +250,25 @@ function withDeclaredExtensionPaths(config: AgentConfig, filePath: string): Agen
 export function editableAgentConfig(agent: AgentConfig): AgentConfig {
 	const { extensions: _extensions, ...withoutExtensions } = agent;
 	const base = agent.override?.base;
+	const description = base?.description ?? agent.description;
+	const frontmatterFields = agent.source === "builtin" || agent.source === "runtime" ? undefined : readAgentFrontmatterFields(agent.filePath);
+	const hasDeclaredField = (...fields: string[]) => frontmatterFields === undefined || fields.some((field) => frontmatterFields.has(field));
+	const withoutSettingsDefaults = (config: AgentConfig): AgentConfig => {
+		if (!frontmatterFields) return config;
+		const next = { ...config };
+		if (!hasDeclaredField("model")) delete next.model;
+		if (!hasDeclaredField("thinking")) delete next.thinking;
+		return next;
+	};
 	const {
 		override: _override,
+		description: _description,
 		output: _output,
 		outputMode: _outputMode,
 		defaultReads: _defaultReads,
 		model: _model,
 		fallbackModels: _fallbackModels,
+		fast: _fast,
 		thinking: _thinking,
 		systemPromptMode: _systemPromptMode,
 		inheritProjectContext: _inheritProjectContext,
@@ -271,26 +283,30 @@ export function editableAgentConfig(agent: AgentConfig): AgentConfig {
 		tools: _tools,
 		excludeTools: _excludeTools,
 		mcpDirectTools: _mcpDirectTools,
+		allowNestedSubagents: _allowNestedSubagents,
 		subagentOnlyExtensions: _subagentOnlyExtensions,
 		mutationTools: _mutationTools,
 		completionGuard: _completionGuard,
+		toolBudget: _toolBudget,
 		...editable
 	} = withoutExtensions;
 	if (!base) {
-		return withDeclaredExtensionPaths({
+		return withDeclaredExtensionPaths(withoutSettingsDefaults({
 			...withoutExtensions,
 			...(agent.extensionsFromDefault ? {} : agent.extensions !== undefined ? { extensions: [...agent.extensions] } : {}),
-		}, agent.filePath);
+		}), agent.filePath);
 	}
 
 	return withDeclaredExtensionPaths({
 		...editable,
+		description,
 		...(base.output !== undefined ? { output: base.output } : {}),
 		...(base.outputMode !== undefined ? { outputMode: base.outputMode } : {}),
 		...(base.defaultReads !== undefined ? { defaultReads: [...base.defaultReads] } : {}),
-		...(base.model !== undefined ? { model: base.model } : {}),
+		...(base.model !== undefined && hasDeclaredField("model") ? { model: base.model } : {}),
 		...(base.fallbackModels !== undefined ? { fallbackModels: [...base.fallbackModels] } : {}),
-		...(base.thinking !== undefined ? { thinking: base.thinking } : {}),
+		...(base.fast !== undefined ? { fast: base.fast } : {}),
+		...(base.thinking !== undefined && hasDeclaredField("thinking") ? { thinking: base.thinking } : {}),
 		systemPromptMode: base.systemPromptMode,
 		inheritProjectContext: base.inheritProjectContext,
 		inheritGlobalContext: base.inheritGlobalContext,
@@ -304,10 +320,12 @@ export function editableAgentConfig(agent: AgentConfig): AgentConfig {
 		...(base.tools !== undefined ? { tools: [...base.tools] } : {}),
 		...(base.excludeTools !== undefined ? { excludeTools: [...base.excludeTools] } : {}),
 		...(base.mcpDirectTools !== undefined ? { mcpDirectTools: [...base.mcpDirectTools] } : {}),
+		...(base.allowNestedSubagents !== undefined ? { allowNestedSubagents: base.allowNestedSubagents } : {}),
 		...(base.extensions !== undefined ? { extensions: [...base.extensions] } : {}),
 		...(base.subagentOnlyExtensions !== undefined ? { subagentOnlyExtensions: [...base.subagentOnlyExtensions] } : {}),
 		...(base.mutationTools !== undefined ? { mutationTools: [...base.mutationTools] } : {}),
 		...(base.completionGuard !== undefined ? { completionGuard: base.completionGuard } : {}),
+		...(base.toolBudget !== undefined ? { toolBudget: base.toolBudget } : {}),
 	}, agent.filePath);
 }