refactor: migrate file processing logic to agent-runtime package #3946

Job	Run time
build-and-check	2m 32s
test-backend	2m 2s
test-packages/agent-runtime	37s
test-.agents	35s
test-common	46s
test-integration-.agents	38s
test-cli	29s
test-npm-app	31s
test-web	28s
test-integration-backend	45s
test-integration-cli	30s
test-integration-common	28s
test-integration-npm-app	31s
test-integration-packages/agent-runtime	34s
test-integration-web	28s
	11m 54s

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