autoformat and 'insert wiki markup' dialog will not convert certain macros such as content-by-user

From advanced macros at least the following macros are affected -

• content-by-user
• index
• junitreport

I think what is going on here is that these macros are of the "ancient" Radeox variety. This means they don't specify whether they have a body or not.

Consequently, if you were to automatically migrate content using these macros during the wiki to XHTML upgrade you could end up discarding page content.
e.g. Take the wiki source -

some text
{content-by-user}
Not body text for the content-by-user macro. Just some text before a second independent instance of the macro.
{content-by-user}
finished

The text between the two 'content-by-user' macro instances would be taken as the body of the macro. And since it doesn't actually store a body this text would be lost.

So to avoid this problem this macro and the others mentioned were not added to the whitelist in wikiToXhtmlMigrationContext.xml (see the macroMigrationManager bean).

However, it is simply an implementation quirk that the usage of these macros in the editor via the wiki markup dialog or autoformatting is broken.