Add --disable-apply-all flag

[lkysow]

Add a flag to disable the use of the command atlantis apply so you
can enforce that each plan must be applied separately.

Notes

• Took @wsoula's commits from Add --disable-apply-all flag #626, squashed, added finishing touches

[codecov]

Codecov Report

Merging #646 into master will increase coverage by <.01%.
The diff coverage is 83.33%.

@@            Coverage Diff             @@
##           master     #646      +/-   ##
==========================================
+ Coverage   72.17%   72.18%   +<.01%     
==========================================
  Files          61       61              
  Lines        4633     4641       +8     
==========================================
+ Hits         3344     3350       +6     
- Misses       1044     1045       +1     
- Partials      245      246       +1

Impacted Files	Coverage Δ
server/user_config.go	100% <ø> (ø)	⬆️
cmd/server.go	79.02% <ø> (ø)	⬆️
server/events/markdown_renderer.go	92.5% <100%> (+0.09%)	⬆️
server/server.go	65.82% <100%> (+0.24%)	⬆️
server/events/command_runner.go	52.94% <60%> (+0.16%)	⬆️

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