This post is just a quick warning that Flyway (before commit 55985b, which includes version 2.0.3, the current version) disables auto-commit on its JDBC Connection. Also, BoneCP (before commit 99d50d, resulting from bug 790585, which includes version 0.7.1.RELEASE, the current version) did not apply the default auto-commit or read-only setting to recycled connections. When these behaviors are combined, connections will be returned from the connection pool which have differing auto-commit. Plan accordingly.

Another quick note, version 0.8.0-rc1 has auto-commit set to false by default, which differs from the JDBC behavior. I consider this a bug.