git 2.1.0, fix bug git-subtree Makefile

Closes #31638.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
git: update 2.1.0 bottle.
sqlite 3.8.6

Closes #31665.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
sqlite: update 3.8.6 bottle.
pandoc-citeproc 0.4; remove old dependencies

Closes #31663.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
pandoc-citeproc: update 0.4 bottle.
Upgrade honors build_bottle? and built_as_bottle options

Closes #31628.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
Do not close inherited file descriptors in compiler wrapper