diff --git a/Makefile b/Makefile
index 7d71d83..682f85a 100644
--- a/Makefile
+++ b/Makefile
@@ -9,6 +9,7 @@ COMMIT_SHA ?= $(shell git rev-parse --short HEAD 2>/dev/null || echo unknown)
 BUILD_DATE ?= $(shell date -u +%Y-%m-%dT%H:%M:%SZ)
 RELSPEC ?= $(shell command -v relspec 2>/dev/null || echo $(HOME)/go/bin/relspec)
 SCHEMA_FILES := $(sort $(wildcard schema/*.dbml))
+MERGE_TARGET_TMP := $(CURDIR)/.cache/schema.merge-target.dbml
 GENERATED_SCHEMA_MIGRATION := migrations/020_generated_schema.sql
 LDFLAGS := -s -w \
 	-X $(BUILDINFO_PKG).Version=$(VERSION_TAG) \
@@ -57,15 +58,19 @@ clean:
 generate-migrations:
 	@test -n "$(SCHEMA_FILES)" || (echo "No DBML schema files found in schema/" >&2; exit 1)
 	@command -v $(RELSPEC) >/dev/null 2>&1 || (echo "relspec not found; install git.warky.dev/wdevs/relspecgo/cmd/relspec@latest" >&2; exit 1)
+	@mkdir -p $(dir $(MERGE_TARGET_TMP))
+	@: > $(MERGE_TARGET_TMP)
 	@schema_list=$$(printf '%s\n' $(SCHEMA_FILES) | paste -sd, -); \
-	$(RELSPEC) convert --from dbml --from-list "$$schema_list" --to pgsql --to-path $(GENERATED_SCHEMA_MIGRATION)
+	$(RELSPEC) merge --target dbml --target-path $(MERGE_TARGET_TMP) --source dbml --from-list "$$schema_list" --output pgsql --output-path $(GENERATED_SCHEMA_MIGRATION)
 
 check-schema-drift:
 	@test -f $(GENERATED_SCHEMA_MIGRATION) || (echo "$(GENERATED_SCHEMA_MIGRATION) is missing; run make generate-migrations" >&2; exit 1)
 	@command -v $(RELSPEC) >/dev/null 2>&1 || (echo "relspec not found; install git.warky.dev/wdevs/relspecgo/cmd/relspec@latest" >&2; exit 1)
+	@mkdir -p $(dir $(MERGE_TARGET_TMP))
 	@tmpfile=$$(mktemp); \
+	: > $(MERGE_TARGET_TMP); \
 	schema_list=$$(printf '%s\n' $(SCHEMA_FILES) | paste -sd, -); \
-	$(RELSPEC) convert --from dbml --from-list "$$schema_list" --to pgsql --to-path $$tmpfile; \
+	$(RELSPEC) merge --target dbml --target-path $(MERGE_TARGET_TMP) --source dbml --from-list "$$schema_list" --output pgsql --output-path $$tmpfile; \
 	if ! cmp -s $$tmpfile $(GENERATED_SCHEMA_MIGRATION); then \
 		echo "Schema drift detected between schema/*.dbml and $(GENERATED_SCHEMA_MIGRATION)" >&2; \
 		diff -u $(GENERATED_SCHEMA_MIGRATION) $$tmpfile || true; \
diff --git a/schema/files.dbml b/schema/files.dbml
index c51b0a7..74062fd 100644
--- a/schema/files.dbml
+++ b/schema/files.dbml
@@ -19,3 +19,7 @@ Table stored_files {
     sha256
   }
 }
+
+// Cross-file refs (for relspecgo merge)
+Ref: stored_files.thought_id > thoughts.guid [delete: set null]
+Ref: stored_files.project_id > projects.guid [delete: set null]
diff --git a/schema/meta.dbml b/schema/meta.dbml
index c59afce..792ccde 100644
--- a/schema/meta.dbml
+++ b/schema/meta.dbml
@@ -27,3 +27,6 @@ Table tool_annotations {
   created_at timestamptz [not null, default: `now()`]
   updated_at timestamptz [not null, default: `now()`]
 }
+
+// Cross-file refs (for relspecgo merge)
+Ref: chat_histories.project_id > projects.guid [delete: set null]
diff --git a/schema/skills.dbml b/schema/skills.dbml
index cc36789..0ea4c3f 100644
--- a/schema/skills.dbml
+++ b/schema/skills.dbml
@@ -40,3 +40,7 @@ Table project_guardrails {
     project_id
   }
 }
+
+// Cross-file refs (for relspecgo merge)
+Ref: project_skills.project_id > projects.guid [delete: cascade]
+Ref: project_guardrails.project_id > projects.guid [delete: cascade]