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Fix duplicate external model generation from directory files #4080

Job	Run time
changes	8s
test-dbt-versions (1.4)	1m 29s
test-dbt-versions (1.5)	1m 47s
test-dbt-versions (1.8)	1m 53s
test-dbt-versions (1.9)	1m 48s
test-dbt-versions (1.10)	1m 44s
test-dbt-versions (1.3)	1m 48s
test-dbt-versions (1.7)	1m 54s
test-dbt-versions (1.6)	1m 39s
test-vscode-e2e	-1s
test-vscode	-1s
migration-test	1m 26s
doc-tests	43s
cicd-tests-windows	11m 25s
style-and-cicd-tests (3.12)	25m 26s
style-and-cicd-tests (3.10)	24m 21s
style-and-cicd-tests (3.13)	24m 45s
style-and-cicd-tests (3.11)	17m 36s
style-and-cicd-tests (3.9)	23m 57s
engine-tests-docker (duckdb)	1m 30s
engine-tests-docker (trino)	8m 58s
engine-tests-docker (mssql)	1m 49s
engine-tests-docker (postgres)	3m 4s
engine-tests-docker (risingwave)	2m 46s
engine-tests-docker (spark)	5m 39s
engine-tests-docker (clickhouse)	2m 45s
engine-tests-docker (starrocks)	2m 38s
engine-tests-docker (mysql)	1m 43s
ui-test	-1s
ui-style	-1s
engine-tests-cloud	0s
	2h 54m 37s