Need to make file writing thread safe

[shaoqx]

the unfinished problem in this commit 8e8bf81 When running multiple mutations in parallel, need to apply thread lock when shared files are writing and wait until its finish.

[shaoqx]

for temp files, we can just create a different if found any is created since they gonna be deleted anyway

[shaoqx]

but for those meant to be shared ones (like ligand parameter files), it is important to make them thread-safe. Need to check if there's anyway to see from the OS if other process is writing this file. Or use a flag file during writing.