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Please see below:
>It's a little difficult to understand.

>I had read the affix.readme before. But it doesn't say
>anything about the PFX ou REP flag. Should we use them
>in our aff file?

PFX is prefix, same rules as suffix but at the beginning of the word.
Yes, you should use it, if your language has prefixes.
For example:
undo  - un is the prefix
impersonate - im is the prefix

REP is the list of easily mixed up characters
for example
ou  au
Helps the spell checker to find fast
and good replacements.

>Also, the .aff file has no comment! Can we add comment
>to that?

Comments must start with #
Do not use comments in the middle of the affix file

>Isn't there a better documentation somewhere?
 The ispell man pages of Geoff Kuennings are
helpful to understand the concept.

Regards, Eleonora

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