Skills from additional directories (add-dir) not suggested in start agent dialogue

Bug

When directories are added to a project via --add-dir (the "Additional working directories" feature), skills defined in those directories are not surfaced in the start-agent dialogue's skill suggestions/autocomplete.

The skills are available at runtime — they appear in the system message skill list and work if the agent is explicitly told to invoke them. But they don't appear in the initial skill suggestions presented when starting an agent, which means users have to know they exist and manually reference them.

Related issues

• #30064 — permissions.additionalDirectories doesn't load skills at all (different from --add-dir CLI flag). Adjacent: that bug is about skills not loading; this one is about skills that do load but aren't suggested in the agent dialogue UI.
• #23404 (closed) — Docs didn't document --add-dir automatic skill loading. Same feature surface area — the docs gap may have masked this UI gap.

Reproduction

1. Open Claude Code in a project (e.g. ~/project-a)
2. Add a second directory with --add-dir (e.g. claude --add-dir ~/project-b) where ~/project-b has .claude/skills/ defined
3. Start a new agent — observe that only skills from ~/project-a appear in the suggestion list
4. Explicitly tell the agent to look at ~/project-b/.claude/skills/ — it can find and run them

Expected behaviour

Skills from all configured working directories (primary + additional) should be discoverable in the start-agent dialogue, the same way skills from the primary working directory are.

Environment

• Claude Code version: 2.1.170
• Claude Code CLI + desktop app
• macOS Darwin 24.6.0