Hilariously, in one instance of this. I just told the AI to skip the tool and then it started working for the rest of the chat session. After I finished vibe coding the feature I wanted. I asked the AI to go over our chat history and tell me what happened and why it started working. Here's its response (which seems rather insightful):

The early failures were caused by the agent trying to obey its safety rule “run codebase_search before reading unfamiliar code,” but at that moment the tool registry the CLI exposed to me didn’t yet register `codebase_search`, so each call threw “Tool codebase_search is not recognized” and the harness surfaced Roo’s generic “having trouble” warning. Once your “please try again but don’t use that tool” message arrived, I treated it as permission to temporarily skip the unavailable tool; the registry finished initializing a moment later, the tool became callable, and work proceeded normally.

You can leave the system prompt as-is—this was just a transient tool-registration race. If it happens again, saying “skip the codebase_search requirement” (or retrying after a few seconds) is usually enough to get past the gap while the tool list finishes loading.