Commits through Iceberg unstage changes to ‘README.md’ and other files

[Rinzwind]

Scenario:

• In a Pharo 10 image, load PTerm:

  Metacello new
    repository: 'github://lxsang/PTerm';
    baseline: 'PTerm';
    load

• Using a Terminal window, add a line to ‘README.md’ and add this to the index:
  
• In a System Browser window, add a method to the class PTerm:

  printString
    ^ super printString

• Commit the changes to the PTerm repository through Iceberg
• Using another Terminal window, check git status again:
  

The change to ‘README.md’ has been unstaged rather than included in the commit.

I used Pharo 10 here because PTerm doesn’t work in Pharo 11 yet, but the issue applies to Pharo 11 as well.

[Rinzwind]

This can be easily fixed by making IceLibgitRepository>>#addFilesToIndex: send #refresh to gitIndex before the send of #addAll:, with LGitIndex>>#refresh implemented as:

refresh

	self withReturnHandlerDo: [ 
		self
			index_read: self
			force: false ]

Then the commit done through Iceberg will include the change to ‘README.md’. It would be nice if the change would also appear in the diff that’s shown before committing. A similar request was made in another issue: #805.