My question was not about duplicate IDs but duplicate entity definitions like
<!ENTITY reference.mhash.functions SYSTEM
[...]
<!ENTITY reference.mhash.functions SYSTEM
pointing to the same file '/opt/phpdoc/en/reference/mhash/functions.xml'
I am wondering about, why this double definitions exists and whats the reason for.
Well, are those definitions both exist in file-entities.ent? Then this is a bug in the generating code, and should be fixed.
Because this double definitions, I assume, let xmllint throw repeating
errors of the same cause.
However, even if you fix the above problem, we will still have multiple entity definitions. This is a standard and XML supported technique. The first entity definition takes precendce, as defined by the standard. We use this to ensure that language dependant entities will work (see fallback near the top of manual.xml). So this is not a problem most of the time. The extract you quoted above is probably an error, and should be fixed.
Goba