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).

internal/httpapi/autonomy.go

@@ -0,0 +1,102 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+)
+
+// ─── Autonomy Settings ─────────────────────────────────────────────────
+
+func (s *Server) GetAutonomySettings(ctx context.Context, req gen.GetAutonomySettingsRequestObject) (gen.GetAutonomySettingsResponseObject, error) {
+	rows, err := s.pool.Query(ctx, `SELECT key, value, version, updated_at FROM autonomy_settings ORDER BY key`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.AutonomySetting{}
+	for rows.Next() {
+		var as gen.AutonomySetting
+		if err := rows.Scan(&as.Key, &as.Value, &as.Version, &as.UpdatedAt); err != nil {
+			return nil, err
+		}
+		items = append(items, as)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.AutonomySetting{}
+	}
+	return gen.GetAutonomySettings200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) PatchAutonomySettings(ctx context.Context, req gen.PatchAutonomySettingsRequestObject) (gen.PatchAutonomySettingsResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	for key, value := range *req.Body {
+		_, err := tx.Exec(ctx, `
+			INSERT INTO autonomy_settings (key, value, version, updated_at)
+			VALUES ($1, $2, 1, now())
+			ON CONFLICT (key)
+			DO UPDATE SET value = EXCLUDED.value, version = autonomy_settings.version + 1, updated_at = now()`,
+			key, value)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	// Re-read all settings.
+	rows, err := tx.Query(ctx, `SELECT key, value, version, updated_at FROM autonomy_settings ORDER BY key`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.AutonomySetting{}
+	for rows.Next() {
+		var as gen.AutonomySetting
+		if err := rows.Scan(&as.Key, &as.Value, &as.Version, &as.UpdatedAt); err != nil {
+			return nil, err
+		}
+		items = append(items, as)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "patch",
+		nil, "PATCH", "/api/v1/policy/autonomy", "",
+		map[string]any{"keys": keysOfMap(*req.Body)}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchAutonomySettings200JSONResponse{Items: items}, nil
+}
+
+// keysOfMap returns the keys of a map[string]string.
+func keysOfMap(m map[string]string) []string {
+	keys := make([]string, 0, len(m))
+	for k := range m {
+		keys = append(keys, k)
+	}
+	return keys
+}