Fix duplicate external model generation from directory files #4027

Job	Run time
changes	7s
test-dbt-versions (1.7)	1m 50s
test-dbt-versions (1.8)	1m 36s
test-dbt-versions (1.10)	1m 44s
test-dbt-versions (1.3)	1m 44s
test-dbt-versions (1.4)	1m 33s
test-dbt-versions (1.9)	1m 44s
test-dbt-versions (1.6)	1m 29s
test-dbt-versions (1.5)	1m 33s
test-vscode-e2e	0s
test-vscode	0s
doc-tests	30s
migration-test	1m 31s
cicd-tests-windows	10m 10s
style-and-cicd-tests (3.9)	22m 19s
style-and-cicd-tests (3.10)	22m 36s
style-and-cicd-tests (3.12)	24m 55s
style-and-cicd-tests (3.13)	16m 55s
engine-tests-docker (mysql)	1m 43s
style-and-cicd-tests (3.11)	23m 2s
engine-tests-docker (mssql)	1m 58s
engine-tests-docker (risingwave)	2m 37s
engine-tests-docker (postgres)	2m 23s
engine-tests-docker (starrocks)	2m 46s
engine-tests-docker (spark)	5m 3s
engine-tests-docker (duckdb)	1m 47s
engine-tests-docker (trino)	8m 27s
engine-tests-docker (clickhouse)	2m 37s
ui-style	0s
ui-test	0s
engine-tests-cloud	0s
	2h 44m 39s

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