I had a look at some old FlashDevleop project files.
So with respect to .air or .exe, the files I edited were:
Building .air
bat/Packager.bat (snippet only, not full file)
:: AIR output
if not exist %AIR_PATH% md %AIR_PATH%
set OUTPUT=%AIR_PATH%\%AIR_NAME%%AIR_TARGET%.air
:: Package
echo.
echo Packaging %AIR_NAME%%AIR_TARGET%.air using certificate %CERT_FILE%...
call adt -package %OPTIONS% %SIGNING_OPTIONS% %OUTPUT% %APP_XML% %FILE_OR_DIR%
if errorlevel 1 goto failed
goto end
bat/PackageApp.bat (snippet only, not full file)
set AIR_TARGET=
Building .exe
bat/Packager.bat (snippet only, not full file)
:: AIR output
if not exist %AIR_PATH% md %AIR_PATH%
set OUTPUT=%AIR_PATH%\%AIR_NAME%%AIR_TARGET%.exe
:: Package
echo.
echo Packaging %AIR_NAME%%AIR_TARGET%.exe using certificate %CERT_FILE%...
call adt -package %OPTIONS% %SIGNING_OPTIONS% -target native %OUTPUT% %APP_XML% %FILE_OR_DIR%
if errorlevel 1 goto failed
goto end
bat/PackageApp.bat (snippet only, not full file)
set AIR_TARGET=-captive-runtime
Building .exe (bundle)
bat/Packager.bat (snippet only, not full file)
:: AIR output
if not exist %AIR_PATH% md %AIR_PATH%
set OUTPUT=%AIR_PATH%\%AIR_NAME%%AIR_TARGET%
:: Package
echo.
echo Packaging %AIR_NAME%%AIR_TARGET%.exe using certificate %CERT_FILE%...
call adt -package %OPTIONS% %SIGNING_OPTIONS% -target bundle %OUTPUT% %APP_XML% %FILE_OR_DIR%
if errorlevel 1 goto failed
goto end
bat/PackageApp.bat (snippet only, not full file)
set AIR_TARGET=-captive-runtime