chore: consolidate endpoints into sessions api

[baxen]

NOTE: this PR is targeting the other branch with session state that we should merge to main first and retarget this

• Remove /agent/* endpoints (agent.rs deleted)
• Remove /action-required/* endpoints (action_required.rs deleted)
• Move all functionality to /sessions/{id}/* namespace
• Rename session.rs to sessions.rs for consistency with route prefix

New session endpoints:

• POST /sessions/{id}/messages/{timestamp}/fork
• POST /sessions/{id}/messages/{timestamp}/edit
• PUT /sessions/{id}/recipe (renamed from user_recipe_values)
• GET /sessions/{id}/tools
• POST /sessions/{id}/tools/{name}/call
• POST /sessions/{id}/resources/read
• POST /sessions/{id}/confirmations
• DELETE /sessions/{id}/extensions/{name}

part 2 of #6251

[Copilot]

Pull request overview

This PR consolidates the API endpoints from the legacy /agent/* and /action-required/* namespaces into a unified /sessions/{id}/* namespace, making sessions the primary client-facing concept while treating agent state as an implementation detail. The change also renames session.rs to sessions.rs and introduces a new reconcile_recipe_state function for idempotent recipe management.

Key changes:

• Removes agent.rs and action_required.rs route modules entirely
• Migrates all endpoints to session-scoped routes with consistent REST patterns
• Introduces idempotent recipe state reconciliation via reset_recipe_state and reconcile_recipe_state

Reviewed changes

Copilot reviewed 21 out of 22 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
ui/desktop/src/utils/providerUtils.ts	Removes unused initializeSystem function and related imports, keeping only substituteParameters
ui/desktop/src/hooks/useRecipeManager.ts	Updates to use updateSessionRecipe API with renamed values field
ui/desktop/src/hooks/useChatStream.ts	Splits editMessage into forkMessage and editMessageInPlace with proper path parameters
ui/desktop/src/components/settings/permission/PermissionModal.tsx	Updates to use getSessionTools with session_id in path instead of query
ui/desktop/src/components/settings/extensions/agent-api.ts	Updates to use session-scoped extension endpoints (addSessionExtension, removeSessionExtension)
ui/desktop/src/components/recipes/RecipesView.tsx	Renames startAgent to createSession for clarity
ui/desktop/src/components/alerts/useToolCount.ts	Updates to use getSessionTools with session_id in path
ui/desktop/src/components/ToolCallConfirmation.tsx	Updates confirmToolAction to use session_id in path parameter
ui/desktop/src/components/OllamaSetup.test.tsx	Adds explanatory comment for skipped tests due to removed initializeSystem
ui/desktop/src/components/ModelAndProviderContext.tsx	Changes to use openSession instead of updateAgentProvider
ui/desktop/src/api/types.gen.ts	Removes old agent/action-required types, adds new session-scoped types with proper path parameters
ui/desktop/src/api/sdk.gen.ts	Removes old agent/action-required functions, adds new session-scoped client functions
ui/desktop/src/App.test.tsx	Updates mock to only include substituteParameters
ui/desktop/openapi.json	Consolidates API spec from /agent/* and /action-required/* to /sessions/{session_id}/*
crates/goose/src/agents/prompt_manager.rs	Adds clear_system_prompt_extras method for recipe state cleanup
crates/goose/src/agents/agent.rs	Adds reset_recipe_state for clearing sub_recipes, final_output_tool, and system_prompt_extras
crates/goose-server/src/routes/sessions.rs	Consolidates all endpoints into sessions namespace with new recipe reconciliation logic
crates/goose-server/src/routes/recipe_utils.rs	Adds reconcile_recipe_state for idempotent recipe application
crates/goose-server/src/routes/mod.rs	Removes agent and action_required modules, renames session to sessions
crates/goose-server/src/routes/agent.rs	Deleted file - functionality moved to sessions.rs
crates/goose-server/src/routes/action_required.rs	Deleted file - functionality moved to sessions.rs
crates/goose-server/src/openapi.rs	Updates OpenAPI documentation to reference session routes instead of agent routes

Comments suppressed due to low confidence (1)

crates/goose-server/src/routes/sessions.rs:520

• The recipe update logic appears duplicated and potentially incorrect. After calling reconcile_recipe_state (line 505), which already builds and applies the recipe with parameter values, the code then calls build_recipe_with_parameter_values again (line 508) with the same inputs. This is redundant and wastes computation. Additionally, reconcile_recipe_state already handles the case where parameters are missing, so the error handling here is unnecessary.