Fix duplicate external model generation from directory files #4010

Job	Run time
changes	6s
test-dbt-versions (1.4)	1m 45s
test-dbt-versions (1.8)	2m 7s
test-dbt-versions (1.6)	1m 48s
test-dbt-versions (1.3)	1m 58s
test-dbt-versions (1.7)	1m 34s
test-dbt-versions (1.10)	1m 55s
test-dbt-versions (1.9)	1m 38s
test-dbt-versions (1.5)	1m 47s
test-vscode-e2e	0s
test-vscode	0s
cicd-tests-windows	11m 8s
style-and-cicd-tests (3.9)	18m 19s
style-and-cicd-tests (3.10)	24m 25s
style-and-cicd-tests (3.11)	21m 30s
doc-tests	49s
style-and-cicd-tests (3.12)	24m 5s
style-and-cicd-tests (3.13)	21m 25s
migration-test	1m 46s
engine-tests-docker (mssql)	2m 11s
engine-tests-docker (mysql)	1m 58s
engine-tests-docker (spark)	5m 44s
engine-tests-docker (trino)	8m 27s
engine-tests-docker (clickhouse)	3m 2s
engine-tests-docker (duckdb)	1m 40s
engine-tests-docker (starrocks)	2m 51s
engine-tests-docker (risingwave)	2m 57s
engine-tests-docker (postgres)	2m 30s
ui-style	-1s
ui-test	-1s
engine-tests-cloud	0s
	2h 49m 23s

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