Having Brown Discharge, Sore Vagina, Itching, Bad Odour. Prescribed Doxycycline Hyclate. What Could This Be?

Hi. I am 20 years old. I have been sexually active since I was 16. I have endometriosis , gets cysts quite frequently, and received the first 2 gardasil shots....About 2 years ago, I started getting this awful brown discharge, brown spotting in between/during periods (I haven t been able to tell the difference since, so I haven t known if I ve even had my period), opening of vagina very sore, itching all over my entire body and a musky odor coming from there and under my arms(not because of poor hygiene , because I shower 2 times a day sometimes even more & wipe from front to back.) I figured it was maybe just all of my lady problems combined,but I got tested for std s anyways. So two years ago I was tested for stds (blood and pap smear ), my gyno or the hospital never called me, so i went up to my gynos office myself. was not able to talk to anyone but the front desk, i told them i had some tests done and she came back and told me everything came back normal....but I still had the same symptoms. I then went to my regular doctor and he gave me medicine for a yeast infection . That did not help. To this day I am still dealing with the same symptoms. I have a new boyfriend of about 1 year & a half and we just had sex for the 1st time about 3 weeks ago, it was very painful and there was some bleeding after. I thought maybe because it had been awhile, but it hurt everytime (felt as though it was being ripped inside, my cervix) & I was still bleeding afterwards. I went to the doctor a week ago, because I was pretty sure I had a UTI, I mean what else could it be? turns out I did have an extreme uti, i was prescribed ciprofloxacin 500 mg, twice daily for 7 days. I went back to the doctor today to get everything checked out, my uti is gone (just need to drink more water, even though its all I drink...) but i was running fever. I then told her about everything involving my lady parts. (Also the irregular discharge, most of the smell, and discomfort dissappeared after take the ciprofloxacin?) she checked for a yeast infection-that was a negative. she then tested me for gonorrhea and chlamydia...even though i was tested before....just incase. and then she did a pap smear. she said i had a massive amount of white/ or clear discharge (not sure which one she said) & that my cervix was inflamed and my white blood cell count in my cervix was way too high...she is pretty sure I have cervisitis? so she said she tested everything and i have to come back in 2 weeks to talk about results and what not. she also prescribed me doxycycline hyclate 100mg 1 tablet twice a day. what could this be???! I m not pregnant either. I m just wondering if this could be anything NOT STD related. please help.