Fixed an apparent error in the CoqEditorHandler.getNextCommand method

This fixes some problems caused by sentences which end with "...", although
not in an entirely satisfactory way -- in particular, adding a full stop to
the end of a sentence should probably cause it to be retracted
Added some explanatory comments to CoqBuilder.buildFiles
Made the Coq builder clean up after deleted files

This change also gets rid of the unhelpful error messages produced when
files were moved around in the workspace
Always strip newline characters from marker error messages

This change makes the Coq editor and the Coq builder present their errors
in the same style
Moved the Coq builder's regular expressions into its companion object

This commit also removes the unnecessary BuildArgs type from CoqBuilder
Include hidden resources when traversing Coq projects

This makes clean builds work properly when output directories are hidden
Improved the robustness of CoqEditorHandler.getNextCommand

Ellipsis handling is now much better than it was, although it's still a bit
too greedy (that is, it accepts more than three full stops as an ellipsis)
Moved the dependency resolution code into the DependencyGraph class
Moved the DependencyGraph class out of CoqBuilder

CoqBuilder is now (slightly) less of a colossal monolith
Removed the last few hard-coded load paths

Even the load path to Charge! is now represented as an ExternalLoadPath
Removed the private CEWrapper object

Its functionality -- running an operation and capturing CoreExceptions in
new IStatus objects -- has moved into the new JobBase companion object
Added copyright statements to a few more source files

Quite a lot of files have no copyright statements at all, which should
probably be fixed at some point
Updated the licence document

This commit updates the copyright years, adds a few additional copyright
holders, and includes a copy of the Apache License, version 2.0, along with
an explanation of the files to which it may be applied
Include the Charge! load path when performing dependency resolution
Use a more specific scheduling rule in the Coq builder

The Coq builder for a particular project now only locks that project rather
than the whole workspace
Removed the Coq builder's debugging messages

The marker- and progress monitor-based feedback mechanisms are now working
quite well
Clear all of a Coq project's problem markers when performing a clean build
Introduced a new kind of marker for Kopitiam problems

Kopitiam removes problem markers rather overzealously at the moment, which
might interfere with other plugins; this new marker type will fix that
Use the Kopitiam-specific problem marker type when manipulating markers
Update the CoqBuilder.stripComments method to use the new parsing method

CoqBuilder.stripComments was originally a modified version of the
CoqEditorHandler.getNextCommand method, which was modernised by commit
9afe0338e8b98461c530f0758e09ca39062e127c