Thanks - just tried an update; looking int these results now.
It looks like you gained .hgignore, and lost .gitignore - suggest leaving both in (for anyone who prefers either git or hg locally);
Also, seem you lost egg-info file.
Other than that, the pull / merge, and a clean checkout of newly updated seem to be the same, but the failed merge might confuse.
Yarko-Tymciuraks-MacBook-Pro-2:tinkerer $ git pull
remote: Counting objects: 3986, done.
remote: Compressing objects: 100% (1189/1189), done.
remote: Total 3986 (delta 2661), reused 3981 (delta 2656)
Receiving objects: 100% (3986/3986), 1.69 MiB | 2.72 MiB/s, done.
Resolving deltas: 100% (2661/2661), done.
+ 7d8909b...92818f8 master -> origin/master (forced update)
+ ff34c9e...70154ed gh-pages -> origin/gh-pages (forced update)
* [new branch] html5 -> origin/html5
* [new branch] release -> origin/release
Auto-merging tinkertest/content/lorem.rst
CONFLICT (add/add): Merge conflict in tinkertest/content/lorem.rst
Auto-merging blog/generate.sh
CONFLICT (add/add): Merge conflict in blog/generate.sh
Auto-merging blog/build-all-themes.sh
CONFLICT (add/add): Merge conflict in blog/build-all-themes.sh
Automatic merge failed; fix conflicts and then commit the result.
Yarko-Tymciuraks-MacBook-Pro-2:tinkerer $ git status
# On branch master
# Your branch and 'origin/master' have diverged,
# and have 4 and 497 different commits each, respectively.
# (use "git pull" to merge the remote branch into yours)
#
# You have unmerged paths.
# (fix conflicts and run "git commit")
#
# Changes to be committed:
#
# new file: .hgignore
#
# Unmerged paths:
# (use "git add <file>..." to mark resolution)
#
# both added: blog/build-all-themes.sh
# both added: blog/generate.sh
# both added: tinkertest/content/lorem.rst
#
Yarko-Tymciuraks-MacBook-Pro-2:tinkerer $ cd ..
Yarko-Tymciuraks-MacBook-Pro-2:tinkerer $ git clone g...@github.com:vladris/tinkerer.git ntinkerer
Cloning into 'ntinkerer'...
remote: Counting objects: 3986, done.
remote: Compressing objects: 100% (1189/1189), done.
remote: Total 3986 (delta 2661), reused 3981 (delta 2656)
Receiving objects: 100% (3986/3986), 1.69 MiB | 2.45 MiB/s, done.
Resolving deltas: 100% (2661/2661), done.
Yarko-Tymciuraks-MacBook-Pro-2:tinkerer $ diff -q tinkerer ntinkerer
Common subdirectories: tinkerer/.git and ntinkerer/.git
Only in tinkerer: .gitignore
Only in tinkerer: Tinkerer.egg-info
Common subdirectories: tinkerer/blog and ntinkerer/blog
Only in tinkerer: build
Only in tinkerer: dist
Common subdirectories: tinkerer/tinkerer and ntinkerer/tinkerer
Common subdirectories: tinkerer/tinkertest and ntinkerer/tinkertest