Update the directory entry writes to use STORE

This patch will break the JarBuilderTest, but I already fixed that in my other branch zundel/super-shady-jar-tool.  It saved 20 CPU seconds in building a large jar file (190MB) and all of that translated into real time savings.  FYI, I did not run these numbers multiple times so treat them with suspicion.

before patch:
real    3m4.610s
user    14m10.336s
sys    0m12.502s

after patch:
real	2m44.933s
user	13m50.587s
sys	0m11.624s