Sometimes it takes a while for codeintel to index a particularly large project, but perhaps that’s not the problem you’re experiencing.
When you get the chance, please go to your ~/.komodoide/9.3/ folder and post the contents of your codeintel.log when your codeintel is not working. That may help us isolate the issue. There’s not much in your e-mail to go on.
Here’s the content of ~/komodoide/9.3/codeintel.log:
WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.langintel:don't know how to get cb detail for 'element' elem WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www2/mail/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www2/flow/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www2/flow/html/inc/mpdf/mpdf.php' has size greater than 1MB (1336667) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www1/mail/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www1/flow/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/www1/flow/html/inc/mpdf/mpdf.php' has size greater than 1MB (1336667) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/dev/mail/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/dev/flow/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918x/dev/flow/html/inc/mpdf/mpdf.php' has size greater than 1MB (1336667) /home/andreas/Komodo-IDE-9/lib/mozilla/python/komodo/textinfo.py:697: ChardetImportWarning: no chardet module to aid in guessing encoding ChardetImportWarning) WARNING:codeintel.manager:File u'/home/andreas/PMPF/20150918/www2/mail/html/admin/crud/phpmyadmin/libraries/tcpdf/tcpdf.php' has size greater than 1MB (1050309)
However, changing the Debug Session Startup Directory to the code folder (or alternatively, changing the Debug Session Startup Directory away from my home folder) seems to have fixed the issue. I have confirmed this for a few projects now.
Or you could just change your “Project Base Directory”, this would effectively mean your project itself lives in a different location than your project file. You can change this setting under Project Preferences.