.github/workflows/pr.yaml

Fix: Only keep refs and sources that exist to match dbt load time behaviour #3025

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Run time

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Job	Run time
test-vscode-e2e	12m 57s
test-vscode	1m 6s
test-dbt-versions (1.3)	1m 35s
test-dbt-versions (1.4)	1m 31s
test-dbt-versions (1.10)	1m 43s
test-dbt-versions (1.5)	1m 43s
test-dbt-versions (1.7)	1m 42s
test-dbt-versions (1.8)	1m 41s
test-dbt-versions (1.6)	1m 34s
test-dbt-versions (1.9)	2m 7s
	27m 39s