fix(mcp): dedupe duplicate search_codebase entry, bump 1.12.0

The tool list registered search_codebase twice: once via SEARCH_CONTEXT_TOOL
constant (old description), once as a literal entry (new description). MCP
clients dedupe by name, so the visible tool count was 17 instead of 18.

Kept the literal entry (it has the updated 'CODE INTELLIGENCE SEARCH'
description that explains the related/definitions enrichment); the dispatch
handler keeps the SEARCH_CONTEXT_TOOL constant reference since they resolve
to the same string.

Also: mcp-setup.md was conflating hosted and local tool sets. The 17-tool
count described hosted only — local exposes a different ~18 tools post-fix.
Rewrote the Tools Reference intro with an explicit table so users stop
comparing apples to oranges, plus a clear 'companies should use hosted'
recommendation that points paying customers at /api/mcp.

Bumped @virsanghavi/axis-server to 1.12.0 to ship the dedup fix plus the
tool optimization batch (propose_file_access userPrompt optional, index_file
disk-read with sensitive-file blocklist + size cap, search_codebase
description rewrite, AXIS_TOOL_LOG audit log, get_project_soul uninit vs
unfilled differentiation).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>