Where is my project explorer window
If you have closed it then you can view it again through window->Show View->Project Explorer. There are many other view options also available here like console, javadoc, search etc.

Relative path in Eclipse
/src is not home folder for project in eclipse. Eclipse see the top level directory of a project as home directory so, if you want to use some input file in project put it in main project folder and then only you can use file name simply to access it in your code.If you want to put the input file in /src then specify /src/filename.
Export tool
If you have a large (high resource consuming) project to run then this tool is very helpful. By file->Export choose Runnable jar file choose a destination name to store it click finish and you are done. You will gate a runnable jar file which can run on any system which has jvm. just do
java -jar filename.jar
or on linux just do
chmod 744 filename.jar
jar file will start executing. If you are using some other file as input then folder containing jar file will be home folder for program so can put other files relative to this home folder.This is java compiler related feature so you can create jar file from command line also same as javadoc feature.