Alright.

The original problem: I have a repo forked from someone else's repo. I am 
taking over maintenance and possible enhancements.

As part of this, and following good coding practice, I have made branches for 
the various things that I have been doing.

I have also made updates to master to bring that branch up to current release; 
the original was based against a library (Forge) at a much older version, and I 
needed to both update to the current version, and update the compilation 
environment so that it would work inside Eclipse properly.

Now, I want to make things put all together. 

I found that if I just did a bunch of merges, I could get something that worked 
with minimal conflicts (two patches that applied to almost adjacent lines 
messed up one merge, and the same changes in a different line order messed up a 
second). It wasn't that hard -- but it left a very messy looking repo.

I want to clean up my repo. That is the goal.

My understanding of best practices for something that you are publishing with 
git for others is to clean up your commits -- rewrite history as the normal 
behavior.

Based on that, I am trying to learn how to rewrite history, and to see what the 
repo looks like when re-written.

> The https://bitbucket.org/keybounce/minecraft-finite-fluids/commits/all 
> appears to give a reasonable display of the current flow if that helps you.

This is nice; I did not know about that. Thank you. 
As I said, it looks messy.

My goal is to learn how to clean up git history.
My understanding based on what I have read/seen so far is that rebase is used 
for that.
My first attempt to understand rebase from the manual was a failure.
My second, based on what you said, did not work the way I understood it to work.

So right now, I would say that I don't really understand how git names the 
sequence of changes on a branch (from when it was split off to the head of that 
branch) (I thought it was just the name of the branch itself) (and I probably 
still don't understand 2 dot vs 3 dot vs no dot), nor how rebase actually works.

Additional information:
1. Most of the branches are short (1 or 2 commits).
2. My understanding of "cleaned up" includes squashing all branches down to a 
single commit when merged into master,
3. My understanding of cleaned up includes: When cleaned up, master should look 
like a bunch of fast forward, as non-fast forwards break other tools (such as 
bisect).

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