Going through things in order, at least the ones that I have something to 
say on:

1 - I haven't seen any. Eventually I my get around to making something.
2 - If you set 'suppressBrowser' to true in settings.json it will not try 
to open up the browser automatically. See 
here: https://github.com/OokTech/TW5-Bob/blob/master/Configuration.md
3 - You can set the location of everything but the root wiki by setting the 
wikisPath setting in the configuration, same link as above. It can be 
absolute or relative, if it is relative it is relative to where the 
executable is.
     Changing the location of the index wiki isn't currently possible 
because the settings are stored in the index wiki and Bob can't load the 
settings without knowing here they are, so using BobEXE it uses the same
     index wiki location  all the time. The plugin version lets you change 
this, but people seem to find that harder to set up and use. I will add an 
issue to look at using a command line argument to set the location of 
     the index wiki.
  3a - Be careful about syncing the tiddlers, you can have Bob and the 
syncing fight over changes to tiddlers. And if you have multiple Bob 
instances editing the same wiki and syncing going on it can get worse.
4 - I don't know about best, but I periodically zip the full wikis folder. 
Eventually I will get around to making an automated back-up for Bob.
5 - .meta files are created by the core server. They are created for any 
tiddler that isn't a normal .tid file, like images
6 - The readme has an incomplete list of features that I think can be 
improvements in the contexts where I use tiddlywiki. The biggest for me are:
  - I can open the same wiki in multiple tabs or on multiple computers 
without worrying about overwriting my edits
  - I can create new wikis easily form within a wiki
  - I can manage many wikis (I currently have over 50 wikis managed using 
Bob on my work laptop)
  - I can use Bob with lots of plugins for editing a wiki and then export a 
single file version of the wiki without any of the plugins included

for the last bit, saving can be much much faster using Bob, loading may not 
necessarily be any faster. But one benefit of Bob is that you can have many 
wikis and have them all easily accessible to each other using a tab in the 
sidebar, so splitting big wikis into smaller more manageable wikis is a 
viable option, for me at least.

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