Ittay,
This could be difficult because you are doing it in retrospect, had you planned to identify the difference between the system and the content from the beginning it would be simpler. I would have no problem with my wikis because I take steps to keep content separate from solutions using naming standards, bundles of tiddlers etc...
- Someone with a lot of experience in tiddlywiki could do a quick job of some of this by identifying macro and template tags, overwritten shadow tiddlers so if you are prepared to share your wiki, they could help get you started (Contact me privately if you want me to have a look, I will respect your privacy, I am a registered business, and well known here) No charge to community members unless it needs too many hours.
- However If you start with a new empty file (then install the bundler plugin with the import bundle activated) , drag the plugins over save and reload and make a copy of this and start to locate some of your customisations and replicate them on the new site it may not take as long as you think.
- The Bunddler plugin will keep a record of the tiddlers you import.
- If you make copies of your wiki as you try something new if it breaks just go back to the previous version.
- You could use the filter [!is[system]] to list all non system tiddlers and start to make inroads as to what you need to remove.
- In the end you have have your own tiddlywiki edition "template" without content you could use for making new Wikis.
This will be a learning process for you as you revisit old customisations but it will give you the opportunity to review them, understand them better and tweek them. The fact is new features and plugins often make customising easier than before so you may find it quicker than you think. I would try and understand what you do rather than just move everything, as tempting as it may be.
Just writing a list of the features you want to keep or see in your new wiki would be a great start because you can ask for help here.
Regards
Tony