Added functionality for ejecting excess compounds from microbes.
Involves a refactoring of emitter components

Exposed AgentComponent to lua

Added exposed AgentComponent to script_bindings.cpp

Add explicit "this->" in SystemWrapper

Just to get it in line with the styleguide.

Catch luabind::error and print a more helpful error message

Added functionality for ejecting excess compounds in Microbe:storeAgent.
Set a lower capacity on energy in player microbe to display the effect.

Moved all compound emission code to AgentEmitterComponent and replaced existing code with calls to emitAgent(...)

Changed emitAgent parameters to include agentId and amount.
Discovered a bug relating to particle lifetime for custom emitter.

Added TimedAgentEmitterComponent for automatic emission of agents instead of that being default

Add Collision system for handling custom events upon collisions.

squashed commits:
Implementation of custom collision events. Some questionable design choices within. (Untested)

Updated collision system to new structure. Now uses CollisionHandlerComponent and CollisionSystem. Manifolds used instead of global callback.

Fixed previous compile error - a new one has taken it's place (uintptr_tr not defined)

Basic working state achieved. m_collisionCallbackKey assignment from lua does not seem to take effect.

Also storage and load still needs implementing, and agentabsorber system needs refactoring.

Storage and load implemented.
AgentAbsorber system & component refactored to use this system.
Acceptance tests performed

Collision filters added, not fully functional

Collision functionality nearly updated.
Needs cleanup, testing and integration with agentabsorber.

Working CollisionFilter class.

Attempt at exposing CollisionFilter to lua. Not successful.

Fixes to improve usage of CollisionFilter. Now uses Collision struct instead of typedef to pair of entityIds.
Better model for exposure to lua (still doesn't quite work).
Cleaned up documentation and header includes.

Fixed minor compile error

Collision system finalized.
- Added a member to Collision to represent the duration of collision represented since last clearCollisions().
  This member will allow more fine grained control of collision handling (damage every 0.5 second, etc).
- Cleaned up documentation and debugging code.

Renamed CollisionHandlerComponent to CollisionComponent.
Added removeCollisionGroup to CollisionComponent.
Added constructor taking a collision group to CollisionComponent

Refactoring of CollisionSystem. Stopped using mutable keyword in collision class and instead uses unordered map.
Added a vector<collision*> mirroring the contents of the unordered_map to allow iteration in lua.

Changed to using boost::map_values for iteration.

Rebased onto master.
Fixed setup.lua
Various relevant fixes.
Code is currently not functioning due to strange bug.

Implementation of custom collision events. Some questionable design choices within. (Untested)

Updated collision system to new structure. Now uses CollisionHandlerComponent and CollisionSystem. Manifolds used instead of global callback.

Fixed previous compile error - a new one has taken it's place (uintptr_tr not defined)

Basic working state achieved. m_collisionCallbackKey assignment from lua does not seem to take effect.

Also storage and load still needs implementing, and agentabsorber system needs refactoring.

Fix typo in Lua script

The previous version crashed because the game state passed to
CollisionFilter's constructor was nil in Lua and consequently
nullptr in C++.

Simplify GameState::findSystem

throw an exception if a reference type is cast, not for pointer
types.

Refactor signature handling of CollisionFilter

Returning a pair of references is a little tricky because it's
not obvious how the std::pair template will handle it. Returning
a reference to a pair, however, is more predictable.

Use static initializers when possible

Minor refactoring

* Use typedefs (i.e. CollisionFilter::Signature) instead of repeating
the type
* Use emplace when possible, it's more readable than constructing
  the collection item manually
* Rename permutation -> combination

Do not register collision filter in Implementation constructor

At that point, the m_impl field of the CollisionFilter is not
initialized yet (because the Implementation object is not
fully constructed). The CollisionSystem asks the filter for
its signature, which is saved in the m_impl object. Since this
doesn't point to anything useful yet, it crashes.

Added CollisionFilter.init and CollisionFilter.shutdown to allow users to create their CollisionFilters in constructors.
Removed debugging code.

Minor refactorings for CollisionFilter and CollisionSystem

Removed typedefs in collision_filter.cpp.

Removed minor error in rebasing

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

Add missing <iostream> include

A fresh Ubuntu 12.04 installation complains about not knowing
std::cerr in scripting/luabind.h when compiling with the mingw
environment. A simple additional include fixes it.

Fixed minor bug and minor adjustment of emission values.
Removed debugging code.

Added meshnames to agent registry, and removed it from every EmitterComponent

Added movement at random ejecting angle

Readded constant size for compounds