Fix remote files handling

[LanderOtto]

This commit fixes several problems with remote ports.

• Fixed error introduced in Fixed remote ports #643. When the remote port was a directory, an exception was thrown at translation time
• CWL SecondaryFile objects were not registered in the DataManager file system
• Function remap_path did not work correctly when the path was not an URI
• In CWL, a Directory object has the listing field to list files and directories. These files can exist or not; in the last case, they are created. Before this commit, when a file existed, it was copied twice: once from the copy of the directory and once from the copy of the file itself.
• Unified the _get_inner_path functions defined in data/manager.py and remotepath.py.
• Fixed the _get_inner_path method of the RemoteStreamFlowPath class. Now it correctly handles data when they are not mounted from the inner location (e.g., when some input data is already stored inside a target container image).
• Fixed the registration of files and directories in the DataManager class when created by the relative functions, i.e., write_remote_file and create_remote_directory in the cwl/utils.py module.
• Improved unit test to check File with secondaryFiles, Directory and literal Directory.

[codecov]

Codecov Report

Attention: Patch coverage is 77.55102% with 22 lines in your changes missing coverage. Please review.

Project coverage is 71.44%. Comparing base (66080a5) to head (2d5ebdf).
Report is 6 commits behind head on master.

✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
streamflow/cwl/utils.py	55.10%	15 Missing and 7 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #648      +/-   ##
==========================================
+ Coverage   71.37%   71.44%   +0.07%     
==========================================
  Files          88       88              
  Lines       11310    11345      +35     
  Branches     1968     1981      +13     
==========================================
+ Hits         8073     8106      +33     
- Misses       2782     2785       +3     
+ Partials      455      454       -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[LanderOtto]

removed the slicing path[7:] in the else branch