I have to agree with Eliot. You need to completely re-think what you are doing. Think of MySQl as a magic black box. Your data goes in, and your data comes out, but you DO NOT TOUCH the database itself. You ASK it questions, and it answers you. You feed it data, and it organizes for you. But, get your hands in the way, and it will bite them off.
If you want to run a local database, you need to install MySQL on your local machine. The Windows version is _NOT_ completely compatible with the Unix version. They are somewhat different. You can move your data UP to the Unix version, but moving DOWN to the Windows version can create some problems (due to Windows, more than anything else).
If you are running Linux on your local machine, you can set up MySQL on your local machine, get your database working, then "mysqldump" it, upload that file, then "mysqlimport" the file into your servers copy of MySQL. This will OVERWRITE any and all data in that database, and create an EXACT COPY of the database from your local machine to the Server's copy of mysql.
During development, this might be what you want, but in operation, this is a _VERY_BAD_THING_ to do.
All Input/Output has to go through the MySQL engine, and you can't play games with it by just adding a few lines on at the end of the database (like the flat file). It won't work. You have to feed the data in, following the rules, let MySQL digest it, and then you can work with it.
There are a number of good books on MySQL and SQL in general. I really wish I had the time to add them to the FAQ....
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