Fix token counting: show only completion tokens, not cumulative prompt+completion ...

The token_count displayed next to assistant messages was summing
prompt_tokens + completion_tokens across ALL tool-calling iterations,
giving hundreds of thousands of tokens for multi-turn conversations.

Now:
- token_count (coins icon) = only completion tokens generated by the model
- context_tokens (ContextBar) = only prompt tokens (context size sent to LLM)

This gives users a realistic measure of how much the model actually generated.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Migrate MCP tool naming from mcp:server:tool to mcp__server__tool ...

The colon separator (mcp:server:tool) confuses many LLMs during
tool-calling because colons appear in schemas and URLs. Switch to
double-underscore separator (mcp__server__tool) for robust parsing.

Key changes:
- navi/mcp/tools.py: add build_mcp_name(), parse_mcp_name(), is_mcp_tool()
- navi/core/tool_executor.py: update _resolve_tool() with new helpers
  and legacy colon fallback for old sessions
- navi/core/tool_utils.py, subagent_runner.py: use build_mcp_name()
- navi/api/routes/{admin,agents}.py: prefix via build_mcp_name()
- navi/tools/{list_tools,reload_tools}.py: migrated
- All profile configs + system_prompt.txt: replace mcp: with mcp__
- manuals/{model_3d,lint_scad,render_3d,spawn_agent}.md: updated
- mcp_servers.d/gnexus-book.json: instructions updated
- docs/{api,profiles,tools,mechanics,visual.html}: updated
- tests: test_tool_executor.py and test_mcp.py aligned

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

SubAgentRunner: filter mcp_servers against subagent_tools whitelist ...

When a profile defines subagent_tools (strict whitelist for sub-agents),
MCP servers were still expanded unconditionally, granting sub-agents access
to MCP tools not listed in the whitelist.  Now:

- If subagent_tools contains mcp:xxx entries, only those specific MCP tools
  are passed to build_tool_list.
- If subagent_tools is non-empty but contains no mcp: entries, mcp_servers
  is set to None — sub-agents get no MCP tools at all.
- If subagent_tools is empty (fallback to enabled_tools), full mcp_servers
  is kept for backward compatibility.

400 passed, 1 skipped

McpTool: auto-inject session_id + normalize navi-3d paths ...

- McpTool.execute() now forces the real session_id from current_session_id
  ContextVar, preventing LLM hallucinations of wrong UUIDs (ghost-session bug).
- For navi-3d MCP server, source_path/output_path are normalized to basename
  to prevent double path nesting when the LLM passes full relative paths.
- Updated MCP tool descriptions to ask for filenames only.
- Added system prompt instructions in context_builder and subagent_runner
  reminding the model to pass bare filenames to navi-3d tools.

396 passed, 1 skipped

Step 4: Extract SubAgentRunner from run_ephemeral() ...

- Create navi/core/subagent_runner.py with full sub-agent loop logic
- Move _iter_stream_guarded to navi/core/stream_guard.py
- Move _check_context_size to ContextCompressor.check_context_size()
- Extract build_tool_list() and load_user_enabled_tools() to tool_utils.py
- Agent.run_ephemeral() becomes a thin wrapper delegating to SubAgentRunner
- Remove ~310 lines from agent.py
- All existing run_ephemeral tests pass unchanged

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>