If your HTC EVO 3D has a newer HBOOT and is rooted but unlocked/S-ON courtesy of HTCDev, then you understand the problems we face. Having to flash kernels and boot animations either separately or via fastboot is a bit of a pain but HTC Dumlock, in conjunction with TWRP 2.0, gets around this limitation.
HTC Dumlock works by flashing a modified TWRP 2.0 recovery image into the boot partition, which runs at a level that allows for flashing of kernels, logos, etc. After recovery is flashed into boot, it can flash your ROM into boot without having to use tools such as Joey Krim's Flash Image GUI before or after new the ROM install.
The downsides to this are 1) to install a ROM, your boot image is flashed twice, which takes some extra time, and 2) if you're a fan of TWRP themes, you can't use them until they are modified to use the HTC Dumlock-enhanced themes.
One bit of oddness is that this flashes a recovery into the boot partition from a program you run. So if you don't flash a ROM, you may be left with recovery as your phone's operating system until such time as you restore that Nandroid we always remind you to make.
[TeamWin] Thanks, Arash Soheili!