refactor: split phase3.go + extract MCP tool registry (R4)

internal/httpapi/phase3.go (2627 lines, 12+ resource domains) split into
15 per-resource files:
- actuator.go: SSH execution machinery (initSSH, sshExec, resolveRunTarget,
  executeApprovedAction, jsonErr, gatewayPreflightPassed, resolveTemplate)
- checks.go, classifications.go, executions.go, approvals.go, patterns.go,
  skills.go, approval_rules.go, autonomy.go, risk_classes.go,
  relationships.go, entity_types.go, metrics.go, agent_activity.go,
  helpers.go — one file per resource domain, each with its own imports.

internal/mcp/server.go: newServer (708 lines, 33 inline tool registrations)
refactored to a registry pattern:
- internal/mcp/tools.go (new): toolReg struct + allTools() returning all 33
  tool definitions. Handler logic moved verbatim — no changes to tool names,
  descriptions, schemas, or behavior.
- server.go: newServer is now 9 lines (iterate registry, AddTool each).
  -699 lines.

No function logic, names, or signatures changed. go vet, build, and all
tests pass (httpapi, mcp, db, policy).

CONTRIBUTING.md

@@ -51,7 +51,7 @@ The app stores credentials via `github.com/zalando/go-keyring` (service: `com.hu
 - Checks Gitea releases every 6 hours
 - System tray → **Check for Updates** triggers an immediate check
 - Download, extract, replace the app in `/Applications`, and relaunch
-- Versions are compared against the `version` const in `main.go`
+- Versions are compared against the `version` var in `main.go`, injected from the repo `VERSION` file at link time (`make desktop` passes `-ldflags "-X main.version=$(cat VERSION)"`)
 
 ## Project structure