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>

Rename MCP tools to mcp:server:tool format and restore human-readable names ...

- Core naming: mcp_server_tool → mcp:server:tool (colon-delimited)
- navi-web tools: search/view/request → web_search/web_view/http_request
- navi-3d tools: compile_scad/render_stl/lint_scad (unchanged names)
- Updated all profile configs, system prompts, docs, manuals, tests
- Added new lint_scad.md manual
- Fixed modeler_3d prompt stale references (scad_lint, model_3d, render_3d)
- All 240 tests pass

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

Clean up remaining web_search / web_view / http_request references ...

- Deleted stale source files: navi/tools/web_search.py, web_view.py,
  http_request.py (no longer imported or registered).
- Updated system_prompt.txt in all profiles (secretary, server_admin,
  discuss, modeler_3d subagent) to reference mcp_navi-web_* tool names.
- Updated key_tools in developer, secretary, server_admin config.json.
- Updated docs (tools.md, profiles.md, api.md) to reflect MCP migration.

Tests: 240 passed.

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

Clarify knowledge persistence prompts

Allow subagents to use selected profiles

Remove tool-call-like examples from prompts

Improve prompt resilience and project context use

Fix profile prompt inconsistencies

Remove context_transfer from all user-facing prompts — internal mechanism only ...

context_transfer is the scratchpad section name used internally by spawn_agent
to auto-inject parent state. Navi doesn't control it and doesn't need to know
about it. Removed from: persona, secretary, server_admin, spawn_agent description,
manual. Internal code (spawn_agent.py) still reads the section transparently.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Fix core subagent misuse: enforce 1 plan step = 1 spawn_agent call ...

Root cause: nowhere was it stated that each AGENT step in the plan
maps to a separate spawn_agent call. Navi was bundling all AGENT steps
into a single call, dumping the full plan on one subagent.

spawn_agent description:
- Lead with: "Delegate EXACTLY ONE step of your plan"
- Explicit: "3 AGENT steps = 3 spawn_agent calls"
- Remove "multi-step sub-task" wording that invited bundling
- briefing: clarify as static context only (credentials, paths, instructions)
  Dynamic findings from prior steps → context_transfer, not briefing

Planning Phase 2 prompt:
- Add AGENT scoping rules: each step = one focused unit, not "do everything"
- Add good/bad examples of AGENT step granularity
- Show multiple AGENT steps in the format example

Secretary & server_admin system prompts:
- Add explicit 1:1 rule with counter-example
- Show correct multi-agent execution pattern with code example
- Clarify briefing vs context_transfer boundary everywhere

Persona:
- "ONE PLAN STEP = ONE spawn_agent CALL" as first sentence in SUB-AGENTS
- Field descriptions tightened: briefing = static, context_transfer = dynamic

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Fix subagent instruction conflicts across persona and profiles ...

Persona:
- Fix [STATUS: completed|limit_reached] reference (format was removed)
- Clarify three fields: task / briefing / system_prompt with distinct roles
- Clarify context_transfer vs briefing: transfer = working state, briefing = credentials

Secretary system_prompt:
- Replace vague "write all context to context_transfer" with explicit field breakdown
- task / briefing / system_prompt each described with their purpose
- context_transfer correctly limited to intermediate findings, not credentials

Server admin system_prompt:
- Same fix: explicit field breakdown for spawn_agent
- Remove dangling "see persona" reference for briefing ending

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Strengthen orchestration mandate: spawn first, inline last ...

secretary/server_admin system prompts:
- Explicit spawning rule: MUST spawn for any sub-task requiring 3+ tool calls
- Additional mandatory triggers listed (research, file processing, remote ops, large output)
- "If in doubt — spawn" as explicit fallback
- AGENT steps: "MANDATORY, never execute inline — defeats the orchestrator model"
- context_transfer pattern: write to scratchpad before spawning, injected automatically

persona.txt:
- Updated SUB-AGENT BRIEFING section: renamed to SUB-AGENTS
- Reflects new context_transfer automatic injection (no longer needs to be in task)
- Added: check [STATUS: ...] in result before deciding next action

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Audit and trim system prompts (~470 tokens saved) ...

persona.txt:
- Shortened personality paragraph (~30% cuts, no content loss)
- Removed duplicate list_tools instruction
- Removed hardcoded 'developer' profile rule (handled by dynamic profiles block)
- Condensed EXECUTION MODES fundamental blockers to one sentence
- Moved sub-agent briefing boilerplate here (single source of truth)
- Trimmed REFLECTION section (tool description handles the how)
- Removed redundant RESPONSE HYGIENE explanation sentence
- Moved 'never assume file exists' into EXECUTION DISCIPLINE
- Removed DOCUMENTATION section

profiles (all three):
- Replaced ~100-token sub-agent briefing boilerplate with pointer to persona
- developer: removed data persistence code block (covered by _template.py)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Add autonomous execution mode; clarify code_exec runs locally ...

persona.txt: EXECUTION MODES section — autonomous mode triggered by user phrase,
handles obstacles independently, only stops on fundamental blockers.

server_admin, developer profiles: explicit note that code_exec / terminal /
filesystem run on the LOCAL machine, never on remote hosts.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Move orchestration from persona to profiles; tune per-profile delegation strategy ...

persona.txt now contains only: identity, profile switching, workspace,
response hygiene, memory, and documentation. All orchestration instructions
removed from the global scope.

Each profile gets its own orchestration model:
- secretary: full orchestrator — delegate any 2+ tool-call sub-task to agents,
  scratchpad as blackboard, todo for milestone tracking
- server_admin: heavy orchestrator — one agent per host / per concern,
  parallel delegation, diagnose-before-act discipline
- developer: builder + research delegation — implementation always inline,
  spawn only for large API/codebase research tasks

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Restructure profiles: directory-based format with config.json + system_prompt.txt ...

Each profile is now a subdirectory under navi/profiles/ containing:
  config.json       — model, temperature, enabled_tools, and other settings
  system_prompt.txt — raw system prompt, editable without touching Python

Added navi/profiles/loader.py for auto-discovery of profile directories.
Removed individual profile .py files (secretary, server_admin, smart_home, developer).
profiles/__init__.py now simply calls load_profiles_from_dir() at import time.

New profiles can be added by creating a directory with the two required files —
no Python changes needed.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>