Here is the configure command that is pretty much the same as in 5.2.6:
So look at the differences ;)
'./configure' '--enable-fastcgi' '--with-mysql' '--prefix=/usr/local/php' '--with-apxs2=/usr/local/apache2/bin/apxs' '--enable-mbstring' '--with-pdo-mysql=/usr/local/mysql/' '--with-mysql-sock=/tmp' '--enable-soap' '--with-zlib' '--with-freetype-dir=/usr/local/lib' '--with-gd' '--with-jpeg-dir=/usr' '--with-png-dir=/usr/lib' '--enable-exif' '--enable-cli'
<snip>
configure: error: Cannot find MySQL header files under yes.
This gives you the clue - it's not "--with-mysql=yes" or something (no idea where "yes" is actually coming from).
Try --with-mysql=/usr/local/mysql
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