fix a bunch more broken, duplicate links and misformatted text

doc/src/Build_extras.txt

doc/src/Build_settings.txt

doc/src/Errors_common.txt

doc/src/Install_git.txt

doc/src/Install_linux.txt

doc/src/Install_svn.txt

doc/src/Packages_details.txt

doc/src/Packages_standard.txt

doc/src/Packages_user.txt

doc/src/angle_cosine_shift.txt

doc/src/fix_deform.txt

doc/src/fix_nve_dot.txt

doc/src/fix_nve_dotc_langevin.txt