refactor: use SeedReferences return value and consolidate reference prompt section

Author: yohamta0

internal/agent/system_prompt.txt

@@ -276,9 +276,9 @@ Rules:
 </memory_management>
 {{end}}
 
+<reference>
 {{if .ReferencesDir}}
-<builtin_knowledge>
-Built-in reference documents are available at {{.ReferencesDir}}/. Use `read` to load them when you need detailed information beyond what `dagu schema` provides.
+Reference documents are available at {{.ReferencesDir}}/. Use `read` to load them when you need details beyond what `dagu schema` provides.
 
 Available references:
 - `schema.md` — Complete DAG YAML schema (top-level and step-level fields)
@@ -292,10 +292,7 @@ Load a reference when:
 - A user asks about a specific executor, CLI command, or env var and `dagu schema` doesn't cover the detail
 - You need to write a DAG that uses coding agents (claude -p, codex exec, gemini -p, etc.)
 - You want to double-check a pitfall before authoring a DAG
-</builtin_knowledge>
 {{end}}
-
-<reference>
 Use `dagu schema` and `dagu example` via bash to look up DAG YAML structure and see examples:
 - `dagu schema dag` — root-level DAG fields
 - `dagu schema dag steps` — step properties

internal/service/frontend/server.go

@@ -180,7 +180,7 @@ func NewServer(ctx context.Context, cfg *config.Config, dr exec.DAGStore, drs ex
 	}
 
 	// Seed built-in knowledge references to data dir (not git-synced).
-	fileagentskill.SeedReferences(
+	referencesDir := fileagentskill.SeedReferences(
 		filepath.Join(cfg.Paths.DataDir, "agent", "references"),
 	)
 
@@ -318,7 +318,7 @@ func NewServer(ctx context.Context, cfg *config.Config, dr exec.DAGStore, drs ex
 
 	var agentAPI *agent.API
 	if agentConfigStore != nil {
-		agentAPI, err = initAgentAPI(ctx, agentConfigStore, agentModelStore, agentSkillStore, agentSoulStore, &cfg.Paths, cfg.Server.Session.MaxPerUser, dr, auditSvc, memoryStore, newRemoteNodeAdapter(remoteNodeResolver))
+		agentAPI, err = initAgentAPI(ctx, agentConfigStore, agentModelStore, agentSkillStore, agentSoulStore, &cfg.Paths, referencesDir, cfg.Server.Session.MaxPerUser, dr, auditSvc, memoryStore, newRemoteNodeAdapter(remoteNodeResolver))
 		if err != nil {
 			logger.Warn(ctx, "Failed to initialize agent API", tag.Error(err))
 		}
@@ -649,7 +649,7 @@ func autoEnableExampleSkills(ctx context.Context, configStore agent.ConfigStore)
 
 // initAgentAPI creates and returns an agent API.
 // The API uses the config store to check enabled status and resolve providers via the model store.
-func initAgentAPI(ctx context.Context, store *fileagentconfig.Store, modelStore agent.ModelStore, skillStore agent.SkillStore, soulStore agent.SoulStore, paths *config.PathsConfig, sessionMaxPerUser int, dagStore exec.DAGStore, auditSvc *audit.Service, memoryStore agent.MemoryStore, remoteResolver agent.RemoteNodeResolver) (*agent.API, error) {
+func initAgentAPI(ctx context.Context, store *fileagentconfig.Store, modelStore agent.ModelStore, skillStore agent.SkillStore, soulStore agent.SoulStore, paths *config.PathsConfig, referencesDir string, sessionMaxPerUser int, dagStore exec.DAGStore, auditSvc *audit.Service, memoryStore agent.MemoryStore, remoteResolver agent.RemoteNodeResolver) (*agent.API, error) {
 	sessStore, err := filesession.New(paths.SessionsDir, filesession.WithMaxPerUser(sessionMaxPerUser))
 	if err != nil {
 		logger.Warn(ctx, "Failed to create session store, persistence disabled", tag.Error(err))
@@ -681,7 +681,7 @@ func initAgentAPI(ctx context.Context, store *fileagentconfig.Store, modelStore
 			ConfigFile:     paths.ConfigFileUsed,
 			WorkingDir:     paths.DAGsDir,
 			BaseConfigFile: paths.BaseConfig,
-			ReferencesDir:  filepath.Join(paths.DataDir, "agent", "references"),
+			ReferencesDir:  referencesDir,
 		},
 	})