merge: Omit generated source columns by default

[tsibley]

Removes default naming template and requires users to explicitly provide their own template to include source columns. This makes the output from an augur merge invocation more self-documenting without columns "magically" appearing. In the expected context of usage within a workflow, the burden of the extra option is negligible. See also discussion on a prior PR.¹

¹ https://github.com/nextstrain/augur/pull/1625#issuecomment-2334501940

Checklist

• [x] Automated checks pass
• [x] Check if you need to add a changelog message
• [x] Check if you need to add tests
• [x] Check if you need to update docs

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 71.06%. Comparing base (db54927) to head (67e756a).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1632 +/- ## ======================================= Coverage 71.06% 71.06% ======================================= Files 79 79 Lines 8268 8268 Branches 2010 2010 ======================================= Hits 5876 5876 Misses 2101 2101 Partials 291 291 ```

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[tsibley]

Once this is merged, I'd like to cut a new (major) Augur release and get it published everywhere so I can then merge https://github.com/nextstrain/measles/pull/52.

[victorlin]

Once this is merged, I'd like to cut a new (major) Augur release and get it published everywhere

If you end up doing this while I'm gone on lab retreat, could you also merge other breaking changes https://github.com/nextstrain/augur/pull/1613 and https://github.com/nextstrain/augur/pull/1629? Those have been approved and I just haven't gotten around to doing the actual release. The only thing is there will be changelog merge conflicts.