Clobber generic/default options with more specific options

[thecjharries]

This fixes an issue where typedoc clobbers the CLI path with the found options from tsconfig.json or typedoc.js. It took me a bit to figure everything out:

• ArgumentsReader has no priority, whereas the priorities for TypedocReader and TSConfigReader are both -100.
• onApi sorts from biggest to smallest. To verify,

[0, -100, -100].sort((a, b) => b - a)
// [0, -100, -100]
new Array(10).fill(0).map((value, index) => index).sort((a, b) => b - a)
// [9, 8, 7, 6, 5, 4, 3, 2, 1, 0]

• Because ArgumentsReader has the largest priority, it executes first. If it encounters an unknown argument, it pushes the filename to event.inputFiles.
• Because TSConfigReader has a lower priority, it executes second. It searches the tsconfig.json for filenames. To do so, it uses parseJsonConfigFileContent, which checks for file specs. If it doesn't find any, it returns files matching **/* that do not match common package folders. In essence, it will always return non-empty fileNames. Even were fileNames empty, event.inputFiles is still clobbered.
• Putting all of this together, this means the usage docs are wrong, as is the index in src/test/renderer/specs/index.html. Unless ArgumentsReader's priority is lowered (or a different solution is used), there's absolutely no way to pass in the source directory/files via the command line.

I've been trying to figure this out for too many hours, so I don't have a demo prepped. I can make one later. This folder structure

/project
    <optional tsconfig.json>
    some-file.ts
    src/
        some-other-file.ts
    docs/

used with this command

typedoc --out docs/ src/some-other-file.ts

will always generate documentation for both some-other-file AND some-file.

[thecjharries]

This should address #527. I didn't think to check the issues until after submitting the PR. I'll search for more after I get some sleep.

[thecjharries]

The branch name isn't as descriptive now. After thinking about this a bit morning this morning, I realized the duplicated priority in TypedocReader and TSConfigReader could, in rare cases, lead to unexpected results.

By changing the priority, the load order is now TSConfigReader > TypedocReader > ArgumentsReader, which allows the most generic to be overwritten by the most specific (e.g. inputFiles start at **/* with a generic tsconfig.json, are replaced by src inside a typedoc.js, and are overwritten by a specified CLI argument).

Applications (and their descendants CliApplications) are bootstrapped via two option reads, allowing generics to be built in order of most to least specific in the first read, then replaced by the desired objects in the second read. Discrete priorities means the order is finally well-defined and the Options will load in a predictable manner.

[blakeembrey]

Thanks @thecjharries!

[beevik]

This commit seems to have broken the processing of the "files" array in tsconfig.json.

See #617