Cleanup file layout.

* Extra top-level directory is unnecessary.
* A directory just for the license is unnecessary too.
* Binaries should not be in a VCS.
Add Linux scripts to compile and run.
Add Settings class.

Currently, it just returns the ImageMagick convert and tesseract
batch files.
Move command-line parsing to Settings class.
Move executable files to a common bin/ directory.

Also, add a wrapper script so that the JAR file can know its location.
Add gitignore file.
Use correct external programs when on Linux.

I kind of assume that only Windows has the bad search path problem.
Maybe an explicit path on Macs would be necessary, but I can't really
check that.
Update README with Linux instructions.
Fix directory separators.
Factor runtimeExecuteAndWait into a Spawn class.
Spawn with array of arguments instead of a string.

I think this is clearer for both programmers and the system. It lets the
system deal with properly quoting each argument, which is different
between Linux and Windows.
Remove unnecessary comments.
Remove strange error message.

I don't know how "unexpected opportunity" means failure.
Simplify file processing using File class methods.
Fix extensions of generated and read files.
Simplify requirement search loop.
Remove extra function isNumber.
Use some Settings directly instead of as arguments.
Remove unnecessary exceptions.

Clearly copy-pasta at work.
Remove unnecessary variables.