Random seed not specified in protocol

Previously, if there was no random seed specified in the protocol file
iDynoMiCS would use zero instead. This new method picks a random seed
that is the product of Math.random() and the system time in
milliseconds.

The random seed is then included in the log file for later reference.
Improved reporting of netGrowthRate

Improved reporting of netGrowthRate when autocatalytic reactions are
involved: we previously used the same estimator as non-autocatalytic
reactions, but this gives the growth rate at the start of the agent
timestep. The new method uses the average growth rate over the agent
time step.

Note that if (agentTimeStep < outputPeriod) then the reported growth
rate will be that of the final agent timestep in the output period and
not the overall growth rate of the output period.
Minor changes

- Eclipse settings updated to Java 1.7
- RunIdyno.py works on Windows
- Bug fix in ActiveAgent.grow()
Merge pull request #45 from roughhawkbit/master

Random seed not specified in protocol
Merge pull request #45 from roughhawkbit/master

Random seed not specified in protocol
Merge pull request #51 from roughhawkbit/pr/2

Merge pull request #45 from roughhawkbit/master
Add IntelliJ files, random.state, results and bin to gitignore
Fix typos in documentation
Refactor SoluteGrid to not use meaningless 'value' variable (Java is garbage collected). Refactor SpatialGrid check for dimensionality to be less confusing
Improve readability by indenting newline
Remove redundant casts, tidy up braces, remove confusing arithmetic
Remove unused variable, minimalTimeStep
Remove useless minus sign, rename variable to something meaningful
Add error message to ReactionFactor
Add species diffusivity.

Add 'diffusivity' param to species, use species grids from agent
container when constructing diffusivity grid.
Refactor if statements
Add diffusivity to output
Move reset of species grid to 0 to fitSpeciesMassOnGrid
Fix, pass simulator to species fit
TODO FIX remove call to calculateComputationDomainGrids before agentgrid is defined