0.29.0 — code-quality refactor (plan E1–E5): file splits, sqlc migration, SSH unification, test coverage

E1: split monolithic files — cmd/nomos (main.go → server.go + mcp.go + workers.go),
    internal/mcp/tools.go → entity_tools/ops_tools/knowledge_tools/analysis_tools,
    internal/httpapi/impl.go → domain files (entities, events, signals, ontology,
    fleet_health, client_context, client_lifecycle, entity_mutations, query_audit).
E2: migrate raw pool.Exec queries to sqlc (entities/relationships queries + generated).
E3: unify SSH — consolidate crypto/ssh dial into actuator/client.go (+client_test).
E4/E5: add tests — db/lifecycle, checkdefaults/build, ontology/preconditions, policy/risk.

internal/httpapi/ontology.go

@@ -0,0 +1,83 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+)
+
+func (s *Server) GetOntology(ctx context.Context, req gen.GetOntologyRequestObject) (gen.GetOntologyResponseObject, error) {
+	resp := gen.GetOntology200JSONResponse{
+		EntityTypes:       []gen.EntityType{},
+		RelationshipTypes: []gen.RelationshipType{},
+		Lifecycles:        []gen.LifecycleDef{},
+	}
+
+	q := sqlcgen.New(s.pool)
+
+	etRows, err := q.ListEntityTypes(ctx)
+	if err != nil {
+		return nil, err
+	}
+	for _, et := range etRows {
+		schemaVersion := int(et.SchemaVersion)
+		var schema *map[string]any
+		if len(et.AttributeSchema) > 0 {
+			var s map[string]any
+			if json.Unmarshal(et.AttributeSchema, &s) == nil && s != nil {
+				schema = &s
+			}
+		}
+		resp.EntityTypes = append(resp.EntityTypes, gen.EntityType{
+			Name:            et.Name,
+			ParentType:      et.ParentType,
+			IsAbstract:      et.IsAbstract,
+			Domain:          et.Domain,
+			Layer:           gen.EntityTypeLayer(et.Layer),
+			Description:     et.Description,
+			LifecycleId:     et.LifecycleID,
+			SchemaVersion:   &schemaVersion,
+			AttributeSchema: schema,
+			Status:          gen.EntityTypeStatus(et.Status),
+		})
+	}
+
+	rtRows, err := q.ListRelationshipTypes(ctx)
+	if err != nil {
+		return nil, err
+	}
+	for _, rt := range rtRows {
+		resp.RelationshipTypes = append(resp.RelationshipTypes, gen.RelationshipType{
+			Name:        rt.Name,
+			Inverse:     rt.Inverse,
+			SourceType:  rt.SourceType,
+			TargetType:  rt.TargetType,
+			Cardinality: gen.RelationshipTypeCardinality(rt.Cardinality),
+			Description: rt.Description,
+		})
+	}
+
+	lcRows, err := q.ListLifecycleDefs(ctx)
+	if err != nil {
+		return nil, err
+	}
+	for _, lc := range lcRows {
+		terminal := lc.TerminalStates
+		var transitions map[string]any
+		if err := json.Unmarshal(lc.Transitions, &transitions); err != nil {
+			return nil, fmt.Errorf("lifecycle %s transitions: %w", lc.ID, err)
+		}
+		resp.Lifecycles = append(resp.Lifecycles, gen.LifecycleDef{
+			Id:             lc.ID,
+			States:         lc.States,
+			DefaultState:   lc.DefaultState,
+			TerminalStates: &terminal,
+			Transitions:    transitions,
+		})
+	}
+
+	return resp, nil
+}