How to convert my code to Linux? Is there an automatic tool for this?
One of the Java key features is portability, so as far as you haven't used any OS-specific code like running a program using CMD or similar or a library that is OS-dependant (which is rare in these times but there are some yet), then you don't have anything to do.
How to deploy my application to the server online (what do I need to copy and to what directory on the web?)
You need to generate a WAR file. This file will zip all your web pages (JSPs) and web resources (js, css, image files) along with the Java binaries (*.class) and libraries (that must be on WEB-INF/lib folder).
Since you're working with NetBeans, here's a Q/A to generate the war file: How can I create a war file of my project in NetBeans?
This war file must be placed in the deploy folder of your web application server. Usually, the hosting provides you the tools (generally a link on the web with user and password) to administrate the host, based on this you should ask (or find it by yourself) the option to upload the war file.
My application writes to a directory on c:drive on my laptop, what should I do to make the application write to correct directory a designated directory on the web server?
You need to configure this path as a constant in your application, or even better, configure it in a properties file (or somewhere else) in order to be read and use it by your application easily. Remember that the path should be generic to be supported in almost every OS. For example, if you use a path with name
C:\some\path\for\files
Its generic form will be:
/some/path/for/files
Since you're going to work on Linux, make sure the user who executes the Tomcat (or the web application server you will use on production) have enough permissions to write on that folder. This can be easily done (and somebody here can fix this please) using the chown
command:
#> chown -R user /some/path/for/files
Here's another Q/A to manage files and path on Java web applications: How to provide relative path in File class to upload any file?