[ENH] Better devops and cleanup

[anibalsolon]

This PR attempts to address some issues with the current repo organization and development flow:

• Environment configuration information is now contained in .env files, which are better for managing: configuration should not be code, tons of infrastructure rely on key-value files, and it is more readable/reliable
• The configuration js file could be easily overwritten in production, so now the separation using .env.dev prevents this
• The package management was confusing, there was a package.json in root, then one in /ui, etc so now each part of the system (api, ui, handler) have their own Dockerfile and package.json
• There were transpiled files (.js) that should not be there, they are generated automatically
• Files uploaded to ezBIDS would have root permission, and if the developer need to use sudo to do something, it's straight wrong. Now, it uses host user ID to run docker, and the data has the correct permissions

⚠️ it requires to stop ezbids containers and rebuild the images
you can stop and rebuild the images using:
./dev.sh stop and ./dev.sh build

[bhatiadheeraj]

Looks great !

[dlevitas]

@anibalsolon, this is causing an error when trying to use quickshear for anatomical defacing.

failed to run deface -- code:1
+ defaced=./quick_nifti_test/time-20200122142947-sn-2-name-anat-T1w.nii.gz.defaced.nii.gz
+ echo '--------------- defacing(quickshear) [0] ./quick_nifti_test/time-20200122142947-sn-2-name-anat-T1w.nii.gz to ./quick_nifti_test/time-20200122142947-sn-2-name-anat-T1w.nii.gz.defaced.nii.gz ----------------'
+ case $method in
+ runROBEX.sh ./quick_nifti_test/time-20200122142947-sn-2-name-anat-T1w.nii.gz ./quick_nifti_test/time-20200122142947-sn-2-name-anat-T1w.nii.gz.mask.nii.gz
environment: line 10: runROBEX.sh: command not found

real	0m0.000s
user	0m0.000s
sys	0m0.000s

[anibalsolon]

Thank you for testing, @dlevitas ! It should be pointing now to the correct file.

[nicoalee]

@anibalsolon handler/bids.sh currently imports ./convert.js. This needs to be changed to convert.ts

[nicoalee]

Some changes need to be addressed as currently:
(1) (IMPORTANT) the finalize step is broken
- convert.js was changed to convert.ts. bids.sh still imports convert.js
- handler/package.json needs to include async in its dependencies
(2) (IMPORTANT) the swagger stuff is broken
(3) (minor) stylistic improvements and consistency with dev files

Addressing my comments should solve these issues

[nicoalee]

if we import controllers like this, then we should export it as default in the controllers.ts file. Instead of module.exports = router it should be export default router

[nicoalee]

include async in dependencies as required by convert.ts

[nicoalee]

are files transpiled into JS when built? Just double checking that the prod script here was intentional and shouldn't instead be: "prod": "tsc && node ./build/ezbids.ts"

[nicoalee]

are files transpiled into JS when built? Just double checking that the prod script here was intentional and shouldn't instead be: "prod": "tsc && node ./build/handler.ts"