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.hsubstate file is skipped from commit. Maybe related to the fact that "hg status" command doesn't show the change of the .hgsubstate file, but committing from the command line commits this file as well.
subrepos are not handled when we commit as: hg ci -m "COMMIT MESSAGE" LIST_OF_FILES - which is exactly what's done from the IDE, we're always commit a file selection and never a whole repository. To correctly support subrepositories "hg ci -m MSG" without any file selection has to be invoked