Make consistent warning/error output across different commands

[aaperis]

Please describe the feature
As a user/admin, I want to have a consistent format for the messages that the cli returns so that I know how to evaluate them/know what to expect when I embed the tool in scripts etc.

Example discrepancy:

./sda-cli decrypt -key alex.sec.pem b/* 
✔ Enter password to unlock private key: 
Decrypting file 1/6: b/file-list-1.c4gh
Warning: file b/file-list-2 is already decrypted, skipping
Warning: file b/file-list-2 is already decrypted, skipping
Decrypting file 4/6: b/file-list-3.c4gh
Warning: file b/file-list-4 is already decrypted, skipping
Warning: file b/file-list-4 is already decrypted, skipping

VS

./sda-cli encrypt -key alex.pub.pem a/* -continue
ERRO[0000] Skipping input file a/file-list-4.c4gh. Reason: input file a/file-list-4.c4gh is already encrypted(.c4gh). 
ERRO[0000] Skipping input file a/file-list-4. Reason: outfile a/file-list-4.c4gh already exists. 
ERRO[0000] Skipping input file a/file-list-2.c4gh. Reason: input file a/file-list-2.c4gh is already encrypted(.c4gh). 
ERRO[0000] Skipping input file a/file-list-2. Reason: outfile a/file-list-2.c4gh already exists. 
ERRO[0000] (4/6) files skipped

Acceptance criteria

• Have a uniform way of returning messages to stdout/stderr (when and if to use fmt.Error, fmt.Print and log.Error).

Additional note
Remember to solve this comment: #451 (comment)
Decide a way in which order the warning/error message should be output

Estimation of size: medium

Estimation of priority: low