Add support for excluding directories and refactor expandInputFiles.

[meowtec]

I am creating this pull request because I have the problem when using TypeDoc.

Command:

typedoc --exclude "**/node_modules/**" --ignoreCompilerErrors --out tsdoc .

Stderr:

ENAMETOOLONG: name too long, stat '/Users/myObject/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser/node_modules/@types/express/node_modules/@types/body-parser'

It was due to a symbolic link recursion, caused by npminstall, a alternative npm install tool, which I have to use for some reasons.

This pull request make isExcluded checking for both directories and files. We can stop the file walking when the directory is excludes. It is also better for IO performance.

[Gerrit0]

Thanks for the contribution! Sorry this took so long to merge.