refactor: extract subdirs list into array
refactor: transform constant to variable
refactor: remove special case for parent dir by moving into loop
avoid custom umask

It's probably better to have directory creation stanardized in
Genome::Sys->create_directory than to have custom permissions in a tool.
Just by coindience Genome::Sys->create_directory uses the same umask.
transform constant to configured variable, GENOME_SYS_UMASK
Merge branch 'AR-271' to move disk permissions to config
Searching on class name here fails, so remove it as a criterion.
bugfix for plotting without clustering
Added extra display tweaks for large numbers of genes
Add legend
updated jenkins submodule to e317612
DB connection details for RDBMS databases is now specified in the Site config modules as env vars
Replace base_web_uri in LegacyConfig.pm with env var GENOME_SYS_SERVICES_WEB_BASE_URL
Add module to make an enviroment variable required
this test had expected and got swapped in the is() tests
Add env var GENOME_SYS_SERVICES_FILES_URL to control base URL for retrieving files
Add env var GENOME_SYS_SERVICES_SEARCH_URL to set the URL that leads to the search page
add env var GENOME_SYS_SERVICES_WEB_VIEW_URL to set the base URL for web views
add env var GENOME_SYS_SERVICES_WIKI_URL to set the URL for the wiki main page
Remove old, unused html templates