How does syncmods actually work?

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Another option:

You could just launch the actual syncmod command line tool from within your IDE.

Syncing the BRL and PUB modules:

c:\program files\blitzmax\bin\syncmods -u username -p password brl
c:\program files\blitzmax\bin\syncmods -u username -p password pub


and the optional ones:
c:\program files\blitzmax\bin\syncmods -u username -p password birdie
c:\program files\blitzmax\bin\syncmods -u username -p password gman
c:\program files\blitzmax\bin\syncmods -u username -p password axe

Using the actual syncmods tool means that it's more likely that your IDE should remain compatible without changes if the syncmod mechanism itself changes at some point in the future.