If you don't want to use command line tools, in other words you want to do it completely within say php or whatever language you are using then why don't you iterate over the tables using SQL itself. for example to check the table structure one simple technique would be to capture a snapsot of the table structure with SHOW CREATE TABLE table_name, store the result and then later make the call again and compare the results.
Have you looked at the source code for mysqldump? I am sure most of what you want would be contained within that.
DC