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/client_context.go

@@ -0,0 +1,88 @@
+package httpapi
+
+import (
+	"context"
+	"strings"
+	"time"
+
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+)
+
+func (s *Server) GetClientContext(ctx context.Context, req gen.GetClientContextRequestObject) (gen.GetClientContextResponseObject, error) {
+	slug := string(req.Slug)
+	_, err := s.resolveEntityID(ctx, slug)
+	if err != nil {
+		return nil, err
+	}
+
+	var version int64
+	_ = s.pool.QueryRow(ctx,
+		"SELECT version FROM context_version WHERE singleton = true").Scan(&version)
+
+	var filesChanged, toolsChanged []string
+	var sopsChanged bool
+	if req.Params.Since != nil {
+		rows, qErr := s.pool.Query(ctx,
+			"SELECT path FROM context_files WHERE last_changed > $1", *req.Params.Since)
+		if qErr == nil {
+			defer rows.Close()
+			for rows.Next() {
+				var p string
+				if scanErr := rows.Scan(&p); scanErr == nil {
+					// Matches tools/setup-*.sh (the auto-setup convention —
+					// see tools/post-pull.sh). Was tools/*.setup.sh until
+					// 2026-07-12, which never matched any real filename.
+					if strings.HasPrefix(p, "tools/setup-") && strings.HasSuffix(p, ".sh") {
+						toolsChanged = append(toolsChanged, p)
+					} else if p == ".sops.yaml" {
+						sopsChanged = true
+					} else {
+						filesChanged = append(filesChanged, p)
+					}
+				}
+			}
+		}
+	}
+
+	if filesChanged == nil {
+		filesChanged = []string{}
+	}
+	if toolsChanged == nil {
+		toolsChanged = []string{}
+	}
+	now := time.Now().UTC()
+
+	return gen.GetClientContext200JSONResponse{
+		AgentFilesChanged: &filesChanged,
+		SopsConfigChanged: &sopsChanged,
+		ToolsChanged:      &toolsChanged,
+		Version:           int(version),
+		Since:             &now,
+	}, nil
+}
+
+func (s *Server) GetClientSecrets(ctx context.Context, req gen.GetClientSecretsRequestObject) (gen.GetClientSecretsResponseObject, error) {
+	slug := string(req.Slug)
+	_, err := s.resolveEntityID(ctx, slug)
+	if err != nil {
+		return nil, err
+	}
+
+	var keys []string
+	if s.secretsManager != nil {
+		list, listErr := s.secretsManager.List(ctx)
+		if listErr == nil {
+			prefix := "clients/" + slug + "/"
+			for _, k := range list {
+				if strings.HasPrefix(k, prefix) || strings.HasPrefix(k, "shared/") {
+					keys = append(keys, k)
+				}
+			}
+		}
+	}
+	if keys == nil {
+		keys = []string{}
+	}
+
+	return gen.GetClientSecrets200JSONResponse{Keys: keys}, nil
+}