I have been an F-1 student since 2002. I have been filing tax with the 1040 form from 2007 to 2011. I was about to file my 2012 tax with the 1040 form again. However, I have just found the following on the IRS web site (Publication 519 (2012), U.S. Tax Guide for Aliens).

Students...
You will not be an exempt individual as a student in 2012 if you have been exempt as a teacher, trainee, or student for any part of more than 5 calendar years unless you meet both of the following requirements.
* You establish that you do not intend to reside permanently in the United States.
* You have substantially complied with the requirements of your visa.

I do intend to reside permanently in the States in the future. As a matter of fact, I am graduating in the Summer and is actively looking for jobs. Does it mean that I must file my 2012 tax with the 1040-NR form? If I use the 1040 file for 2012, will have have problems in the future when I apply for my permanent residency?

Looking forward to hearing from you. Thank you very much.

There is also the life time look back rule for F/J students. If you were exempt as a students for 5 years since January 1 st, 1985, you cannot be exempt again.

You are CLEARLY a resident alien for tax purposes, and have been since 2007.

Continue to file as a resident.