Add restart functionality

[edoddridge]

This PR implements a restart feature - given the appropriate checkpoint files and value for niter0 the model will continue with a simulation.

There is no requirement that parameters, apart from domain size, remain consistent between runs. The restarted simulation takes in parameters in exactly the same way as a normal run - i.e. through the call to driver.simulate or the aronnax.conf file.

Other small changes:

• the output directory is no longer wiped clean when starting a simulation (since restarting in a directory shouldn't delete data)
• checkpoint files are dumped at the end of every simulation, as discussed in #118
• the writeoutput` subroutines now have to be told which folder to write into (this change wasn't needed in the end, but seems like a better default so I left it)

[codecov[bot]]

Codecov Report

Merging #160 into master will increase coverage by 0.26%. The diff coverage is 98.38%.

@@            Coverage Diff             @@
##           master     #160      +/-   ##
==========================================
+ Coverage   94.09%   94.36%   +0.26%     
==========================================
  Files           5        5              
  Lines        1134     1206      +72     
  Branches       57       61       +4     
==========================================
+ Hits         1067     1138      +71     
  Misses         52       52              
- Partials       15       16       +1

Impacted Files	Coverage Δ
aronnax/driver.py	93.45% <100%> (ø)	:arrow_up:
aronnax.f90	94.62% <98.37%> (+0.34%)	:arrow_up:

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