fix: resolve issues #1888, #1693, #1891

- fix(hooks): skip todo continuation when agent has pending question (#1888)
  Add pending-question-detection module that walks messages backwards
  to detect unanswered question tool_use, preventing CONTINUATION_PROMPT
  injection while awaiting user response.

- fix(config): allow custom agent names in disabled_agents (#1693)
  Change disabled_agents schema from BuiltinAgentNameSchema to z.string()
  and add filterDisabledAgents helper in agent-config-handler to filter
  user, project, and plugin agents with case-insensitive matching.

- fix(agents): change primary agents mode to 'all' (#1891)
  Update Sisyphus, Hephaestus, and Atlas agent modes from 'primary'
  to 'all' so they are available for @mention routing and task()
  delegation in addition to direct chat.

src/agents/atlas/agent.ts

@@ -30,7 +30,7 @@ import {
   buildDecisionMatrix,
 } from "./prompt-section-builder"
 
-const MODE: AgentMode = "primary"
+const MODE: AgentMode = "all"
 
 export type AtlasPromptSource = "default" | "gpt" | "gemini"
 

src/agents/hephaestus.ts

@@ -19,7 +19,7 @@ import {
   categorizeTools,
 } from "./dynamic-agent-prompt-builder";
 
-const MODE: AgentMode = "primary";
+const MODE: AgentMode = "all";
 
 function buildTodoDisciplineSection(useTaskSystem: boolean): string {
   if (useTaskSystem) {

src/agents/sisyphus.ts

@@ -8,7 +8,7 @@ import {
   buildGeminiIntentGateEnforcement,
 } from "./sisyphus-gemini-overlays";
 
-const MODE: AgentMode = "primary";
+const MODE: AgentMode = "all";
 export const SISYPHUS_PROMPT_METADATA: AgentPromptMetadata = {
   category: "utility",
   cost: "EXPENSIVE",