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update-texmf is a shell script to generate /etc/texmf/texmf.cnf from files in /etc/texmf/texmf.d/*.cnf
The tex-common provides 05TeXMF.cnf to 95NonPath.cnf and we assume that other TeX related packages should use the name only with the lower cases. The two digit numeral determines the order in which update-texmf read a file.
A user who wants to customize /etc/texmf/texmf.cnf should add, for example, 22mymacro.cnf in /etc/texmf/texmf.d/ and run 'update-texmf'. Thanks to ucf(1) update-texmf will regard manual changes of /etc/texmf/texmf.cnf, however it is recommended to change the files in /etc/texmf/texmf.d/ and to generate /etc/texmf/texmf.cnf.
Further information can be found in /usr/share/doc/tex-common/README.Debian.{txt,pdf.shtml}