[ENH] configurable timeouts for command execution

Allows configuration of command execution timeout from default 3600 seconds to a custom value. Might also specify that as a clone/cloneandupgrade command option. Note: since commands can be run in many different contexts (one by one via local/ssh adapter host libs runCommand or runCommands to run many or just run string commands), I decided to use a global ENV much like temp folder and other env variables to make sure all command executions use the same defined timeout.