[upload] the `-continue` flag does not work when recursively encrypting and uploading folders

[nanjiangshu]

Describe the bug
When there exist c4gh files in the folder, the -continue flag does not work when recursively encrypting and uploading folder(s). That is, instead of ignoring already uploaded files and continue, the command is aborted with the following error when it encounters an existing c4gh file.

ERRO[0000] Skipping input file test_dataset_small/dummy_1.txt. Reason: outfile test_dataset_small/dummy_1.txt.c4gh already exists. 
Error: aborting

Steps to reproduce
Start the SDA integration test and download s3cmd-inbox.conf and run docker cp verify:/shared /tmp/

Upload a folder containing some files by sda-cli, for example

sda-cli -config s3cmd-inbox.conf upload -r -encrypt-with-key  /tmp/shared/c4gh.pub.pem test_dir1

and break in the middle

Then run

sda-cli -config s3cmd-inbox.conf upload -r -encrypt-with-key  /tmp/shared/c4gh.pub.pem test_dir1 -continue

Note that the flag -continue works when uploading without the -encrypt-with-key flag.

Expected behavior

• The command should ignore already uploaded files and continue the process when the flag -continue is used, either with or without the -encrypt-with-key flag.
• Tests verifying the fix are added

Additional context

Estimation of size: small/medium/big

Estimation of priority: low/medium/high

[aaperis]

The functionality that is requested here was not implemented by choice. Imagine, for example, the user providing a different pubkey when using the -continue flag. I still think this should not be implemented.

The -encrypt-with-key first calls encrypt that encrypts all files and then calls upload that uploads them. The -continue flag is part of the upload module, meaning that it is not there to resume encryption but only uploads.
If the process fails during encryption, then other ways need to be followed or a different flag targeting encrypt should be implemented.
If the process fails during upload (after encryption step) then -continue can be used to resume the upload as intended.