When the aclocal, automake, or autoconf Project menu actions are chosen, the tool is being run for the project directory. This is incorrect. The tool should be run with the current selected directory being the CWD.
Fixed in next release. The CWD is now correctly calculated and used when the commands are executed. The CWD is displayed for aclocal and automake when prompting for the options as this has bearing on the actual options used (e.g. relative directories). A new success dialog is now shown for all 3 tools. For autoconf, the success dialog shows the CWD it was successfully run in.