Update manifest when file deleted on disk (#1089) #5118

Job	Run time
Unit tests with race condition detection	2m 45s
Unit Tests	2m 24s
Lint	4m 28s
Build Unsigned Snapshot	2m 0s
Performance Tests	4m 58s
Integration Tests - Official OSS Images (bookworm, mainline, debian)	7m 27s
Integration Tests - Official OSS Images (bookworm, stable, debian)	7m 38s
Integration Tests - Official OSS Images (alpine, stable, alpine)	7m 18s
Integration Tests - Official OSS Images (alpine, mainline, alpine)	7m 25s
Integration Tests - Official Plus Images (alpine, 3.20, r32, alpine, /nginx-plus/agent)	7m 33s
Integration Tests - Official Plus Images (alpine, 3.19, r31, alpine, /nginx-plus/agent)	7m 18s
Integration Tests (redhatenterprise, 9)	10m 21s
Integration Tests - Official Plus Images (debian, bookworm, r32, debian, /nginx-plus/agent)	7m 57s
Integration Tests - Official Plus Images (debian, bookworm, r31, debian, /nginx-plus/agent)	7m 42s
Integration Tests (ubuntu, 22.04)	11m 9s
Load Tests	5m 12s
Integration Tests (alpine, 3.19)	8m 6s
	1h 51m 41s

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