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fix(agent): guard apply_patch with secret-guard and realpath bound #3146

Job	Run time
static-analysis	46s
test (4/4)	29s
build	9s
test (1/4)	52s
test (3/4)	1m 28s
test (2/4)	54s
test (one-process pollution detector)	-1s
eslint	3s
typecheck	2s
prettier	2s
build-and-test	3s
test (src)	3s
	4m 50s