Add ProcessOrganelle for converting compounds
Closes #41

squashed commits:
Add ProcessOrganelle for converting compounds

Closes #41

Add ProcessOrganelle

Fixed syntax in process_organelle.lua and added hasInputAgent method to ProcessOrganelle class

Added ProcessOrganelle support into Microbe class, and added process_organelle.lua to manifest

Added code to setup.lua to test ProcessOrganelle (currently not working)
Minor fixes to ProcessOrganelle related code in process_organelle.lua and microbe.lua

Minor formatting and reintroduced function missing in process_organelle.lua

Fix some minor errors in the ProcessOrganelle script

* Use table.insert instead of a[#a+1] to not repeat the table name
* Call superclass' constructor in ProcessOrganelle.__init
* Explicitly pass self to Organelle.update in ProcessOrganelle.update
* Lua has no -= (or += for that matter)
* Typos

Fixed error in loading a savegame with ProcessOrganelle.

Removed debugging code in microbe.lua

Created cooldown system for Process organelles, limiting the frequency of agent absorbtion and production

Fixed missing local specifier on two variables in process_organelle.lua

Implemeneted colours for process organelles to reflect how filled it is. Also minor bugfixes

Move "local" to where it belongs

Made distribution of agents, dependant on time elapsed instead of frames. (1 agent per agent type distributed per 100ms)

Release candidate 1 Done.

- Fixed compile error
- Removed debugging code
- Changed setup of compounds/agents to reflect mitochondrion

Added additional documentation for processing compounds.
Minor refactoring to compound distribution for more accuracy.

Replaced magic value with proper constant

Re-changed emitters to use new oxygen, glucose, atp, co2 system.
Cleanup of old variable and comment names in setup.lua