chore: upgrade to Bun 1.3 #3940

Job	Run time
build-and-check	2m 41s
test-backend	42s
test-packages/agent-runtime	30s
test-common	35s
test-npm-app	39s
test-.agents	29s
test-web	36s
test-integration-cli	27s
test-integration-npm-app	35s
test-cli	27s
test-integration-packages/agent-runtime	29s
test-integration-backend	35s
test-integration-web	29s
test-integration-.agents	34s
test-integration-common	28s
	10m 16s

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