There are good things that can come from staying.
If (when, really) the productivity gains come, management
will notice and you'll be known as that person who improved things. This will give you good favour.
And if it doesn't work out, next time you get asked in interview, "What are some challenges you have faced?" you can talk about how you introduced Git and JIRA to a company that didn't have source control and bug tracking. You can talk about how you tried to change a company culture from hand-editing files in production to having deployment scripts. You can talk about the challenges you faced. It gives you a clear answer to "Why are you leaving?", you can talk honestly about your expectations in terms of what a company should provide for its developers, talk about how your current company isn't or wasn't meeting those and use that to indirectly talk about how much of the joel test the prospective company can meet.
It will give you a fresh sense of perspective too. In the future when you're struggling with a build system you can think, "well at least we're better than we were at Initrode".
And maybe it's just a really nice place to work, not all work is about being as efficient as possible at all times. Sometimes you can stand back and realise that while other teams could do what you're doing in half the time, you're still getting paid to do this job and maybe your colleagues are warm and friendly.