(feat): add --preserveModules flag

[agilgur5]

• this works the same way as Rollup's preserveModules option, leaving
  the module structure and not bundling any files together
  • format, env, and minify are used as directories instead of filename
    suffixes since the filename can't be changed without configuring
    output.entryFileNames (possibly a future improvement?)

Fixes #276, fixes #299, fixes #321 .
Might fix ##382 , but need to think about what to do with index.js.
Related to #367, #175, #365, #425

Things to Review / TODOs:

• add docs
• declaration files are currently duplicated in each format directory. I'm not sure if this is a problem or not. Changing this requires something like setting declarationDir (conflicts/depends on (fix): declarationMaps (*.d.ts.map) should have correct sources #488) and then not producing types multiple times (conflicts/depends on (fix): multiple entries should output multiple bundles #367)
• dist/index.js is still created. I'm not sure if it still makes sense to have (related to Ability to disable creating CJS dist/index.js file #382). If it does, its content needs to be modified (conflicts/depends on (fix): multiple entries should output multiple bundles #367) and maybe its location should be changed to dist/cjs/index.js?

[agilgur5]

I'm thinking that -- in the future as it would be very breaking -- it might make sense to have TSDX eventually use outDir and outFile to determine whether to use preserveModules or not. That way there's no flags to configure, it just follows whatever you have in your tsconfig.json