[FT-384] Automate loading of TCGA OV aCGH data

TCGA OV clinical data is also included
If PGHOST is unix socket, use localhost for jdbc
config: do not redefine vars in insertions
grailsSettings is unavailable when running WAR in tomcat
Fix small syntax error
Fix handling of PGHOST conversion

I had forgotten to commit host_fixup.php. I took the opportunity to
move host_fixup.php and bring the PGHOST fixup to
gen_kettle_properties.php as well.
Add targets for installing deps & generating vars

In Ubuntu
Added target to minimize diffs in data files
Update st_password.sh for bcrypt
Fix config for dev mode
Change some log levels for less verbose startup
Fix version in application title
Fix logout url when used with auto-login
Reduce logrounds for bcrypt

15 is too slow. Also removed salt property, which is not used for
bcrypt.
Fix & improve minimize_diff
Fix passwords fos ts users given bcrypt change

Password for admin user is admin. For the rest of the users, change
their passwords (possibly with the script included).
Add some dummy recipes for autocompletion
Improve minimize_diff target

Mainly more diagnostics.
Add .gitignore in R/
Revert "Sync with transmart/transmartApp-DB"

This reverts commit dfb62d7693e68cfd80a5071f9212c0149b3f865e.
We don't want no duplicated analyses after all.