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/db/queries/entities.sql

@@ -44,6 +44,36 @@ UPDATE entities SET
 WHERE id = sqlc.arg('id') AND version = sqlc.arg('version')
 RETURNING *;
 
+-- name: MergeEntityAttributes :execrows
+-- Shallow-merge a JSON patch into an entity's attributes (the
+-- update_entity_attributes MCP/HTTP surface). Replaces the raw
+-- `attributes = attributes || $2::jsonb` used in entity_tools.go.
+UPDATE entities SET
+    attributes = attributes || sqlc.arg('patch')::jsonb,
+    updated_at = now()
+WHERE slug = sqlc.arg('slug');
+
+-- name: SetEntityState :execrows
+-- Set an entity's lifecycle state by id (the set_entity_state surface, run
+-- after db.ValidateTransition). Replaces the raw
+-- `UPDATE entities SET state = $2 ... WHERE id = $1`.
+UPDATE entities SET
+    state = sqlc.arg('state'),
+    updated_at = now()
+WHERE id = sqlc.arg('id');
+
 -- blast_radius(): the recursive-CTE traversal function's TABLE return type
 -- is opaque to sqlc's analyzer — that one query stays hand-written pgx in
--- internal/httpapi (see impl.go).
+-- internal/httpapi (see entities.go GetBlastRadius).
+--
+-- Deliberate raw-SQL exceptions (plan E2): the httpapi entity *read* handlers
+-- (ListEntities/GetEntity/GetGraph/queryEntities) project a fixed
+-- `entityCols` column set (entities.* + a LEFT JOIN to entity_status for
+-- health/last_check_at) and scan it positionally into the oapi-generated
+-- gen.Entity shape. sqlc generates its own row struct per query and cannot
+-- emit gen.Entity, so migrating those reads would add a per-call field-by-
+-- field mapping with no compile-time gain and real column-order risk. They
+-- stay hand-written pgx, like blast_radius and the seed/export bulk paths
+-- noted in sqlc.yaml. The mutation/relationship surface (MergeEntityAttributes,
+-- SetEntityState, InsertRelationshipIfAbsent, EndCurrentRelationship) IS
+-- migrated and is what the entity CRUD tools now call.

internal/db/queries/relationships.sql

@@ -25,3 +25,18 @@ ORDER BY r.type, se.slug, te.slug;
 -- name: EndCurrentRelationship :execrows
 UPDATE relationships SET valid_to = now()
 WHERE source_id = $1 AND target_id = $2 AND type = $3 AND valid_to IS NULL;
+
+-- name: InsertRelationshipIfAbsent :execrows
+-- Idempotent relationship insert (the create_relationship surface): no-op if
+-- an active edge of the same source/target/type already exists. Replaces the
+-- raw INSERT...WHERE NOT EXISTS used in entity_tools.go.
+INSERT INTO relationships (source_id, target_id, type, attributes, valid_from)
+SELECT sqlc.arg('source_id'), sqlc.arg('target_id'), sqlc.arg('type'),
+       sqlc.arg('attributes')::jsonb, now()
+WHERE NOT EXISTS (
+    SELECT 1 FROM relationships
+    WHERE source_id = sqlc.arg('source_id')
+      AND target_id = sqlc.arg('target_id')
+      AND type = sqlc.arg('type')
+      AND valid_to IS NULL
+);