docs: architecture documentation updates for M0

[rplunger]

Goal

Consolidate and track all architecture documentation improvements identified during the system architecture definition and agent-native audit. These are polish tasks that should be done alongside implementation milestones, not blocking them.

Checklist

From architecture audit (#48):

• Align vision module docs with capability-based features (was docs(architecture): align vision module with capability-based features #42)
• Document health endpoint and tracing per ADR-004 §13 (was docs(architecture): document health endpoint and tracing per ADR-004 §13 #43)
• Add deferred security items and threat model to security.mdx (was docs(architecture): add deferred security items and threat model clarity to security.mdx #44)
• Create single canonical source for API routing matrix (was docs(architecture): single canonical source for API routing matrix #45)
• Add "How to add an adapter" checklist (was docs(architecture): add "How to add an adapter" checklist #46)
• Glossary links and architecture index polish (was docs(architecture): glossary links and architecture index polish #47)

From module review:

• Review and update Core Engine domain ports and Excalidraw (was docs(core): review and update Core Engine domain ports and Excalidraw #65)
• Review and update API Engine domain ports and Excalidraw (was docs(api): review and update API Engine domain ports and Excalidraw #66)
• Update Excalidraw port styling globally (was docs(architecture): update Excalidraw port styling globally #67)
• Review Inference Engine domain documentation (was docs(inference): review Inference Engine domain documentation #68)
• Review Peripherals Engine domain documentation (was docs(peripherals): review Peripherals Engine domain documentation #69)

From agent-native audit (#59):

• Add "What the device can do" page and document GetCapabilities (was docs(guides): add "What the device can do" page and document GetCapabilities #55)
• Document prompt composition (system prompt + dynamic context) (was docs(inference): document prompt composition (system prompt + dynamic context) #57)
• Document MCP Server tools as 1:1 primitives design discipline (was docs(api): MCP Server tools as 1:1 primitives (design discipline) #58 -- also tracked in M0.2 MCP server issue feat(api): implement MCP server #91)

From roadmap:

• Finalize roadmap and update README (was docs(project): finalize roadmap and update README #70)

Approach

Work through these incrementally as each milestone completes. No need to do all at once.