Fix #101, implement new way to handle beaker conf with user prefs
Before this change the beaker.conf.json file will only be copied
to the .beaker directory, when one file doesn't exist already. After
this change, such copying operation won't take place anymore. Instead, a
beaker.pref.json file in the dot directory will be used to record user
preferences. And the final configuration beaker uses would be the merged
result of the beaker.conf.json (in install dir) overridden by
beaker.pref.json (in .beaker). Also, removing elements from arrays is
possible by by prefixing array property name with "_remove-".
Minor, add newline to the end of file
Change the to remove prefix
Merge pull request #376 from twosigma/alee/fix-101

Fix #101, implement new way to handle beaker conf with user prefs
About #360, make 'outputDisplay' event logged to GA
Only log 'outputDisplay' events when result type is defined to reduce noise in analytics reports
removing xcuserdata again
add .DS_Store (generated by mac finder)
base version string off branch instead of tag
add script to install dependencies
make all dependencies install without prompting except java
add julia
copy nginx into our install directory on windows and run it out of there (like mac does)
move working dir and add file extension to zip name.  why are these required? it worked before....
do not run windows code on linux
included jre works
now works with included python
correct 7za command
add stripped python (many but not all used files removed)
Merge branch 'v0.55' of https://github.com/twosigma/beaker-notebook into v0.55