Tool list access consolidated into a shared toolCatalog

What

• The code that builds the tool permission context (which tools are allowed/disallowed, including --tools narrowing) now receives getAllBaseTools as an explicit parameter instead of calling a fixed global function directly.
• Session and agent setup (main loop, subagents, resumed sessions) now threads a shared toolCatalog object ({ getAllBaseTools, getTools, assembleToolPool }) through options, alongside the existing tools field, replacing scattered direct calls.

Why This is an internal cleanup that makes tool-list access consistent and explicit across the codebase, reducing the chance of different code paths using mismatched or stale tool lists.