Wow, a lot of good questions here. Let me see if I can answer them all. People wiht more knowledge, please feel free to correct me if I'm wrong. Here goes...
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TSOP ISSUES
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Q: "Can I flash my TSOP/BIOS with this Free-X/EvoX (Pheonix) hack?"
A: No. Unfortunately, to do this you would need to solder two jumpers on your X-Box main board (D9 and D0) together. As of now, there is no way (under Win32.. the EASIEST platform to do this stuff on... sorry Linux), however I have heard this is being looked into. It IS possible. Just not public YET. Give it a week or so.
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RESETTING ISSUES
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There were a few questions regarding this. Basically, let me tackle a few known issues with reset, and then explain what is/isn't (or just a bug STILL) normal.
WHAT IS FINE:
1.) Selecting "MS Dashboard" WILL cause the X-Box to reboot. I cant go into too much detail RIGHT NOW (I'm at work on "Unscheduled Break" ... it's my last day here... so whatever hehe) but as soon as I get home (around 2:45 AM EST) I will edit THIS portion of the post with WHY this is normal. My challenge in the meantime is to simply THINK about what you have done. I mean you replaced the default .xtf files which are what the original dash/kernal are dependant on. So what would happen if you got rid of them and then TRICKED the X-Box (like we've been doing) by replacing them??? Ahhhh now you get it

WHAT IS "NOT" FINE (NOT FIXED STILL):
1.) Reset on EJECT. If you have followed my instructions exactly, and have a v1.0/1.1 and a 4034 Kernal and 4922 "BIOS"/Dash, you should STILL notice the X-Box reboots when you press EJECT at any give time. This is no big deal, as it will just bring you back to EvoX. Meh... This may be a error in my ways or still the old bug that reared it's ugly head back in the original "4034" intended Kernal hacks for EvoX they have since repaired (remember.. using this hack we are "backdating" ourselves with these hacks... so the OLD bugs will have to be re-worked out)
2.) Stored App's causing a reset on some boxes. Once I have more info on this, I will update. I will read more tonight, but as of yet... this seems to be X-Box dependant. I have yet to experience this issue. I have a few X-Box's ... so I might just fuck with one of them and try to cause issues on it that would replicate this setup. I will update with more info. But, as far as I know... this shouldn't happen.
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BORN AGAIN VIRGIN X-Box's
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It IS indeed possible to put your X-Box back to it's original state if you indeed backed up the ORIGINAL Xbox.xtf and Xbox Book.xtf files. Simply replace the renamed "bert.xtf" and "Snuffleupagus.xtf" files (which should be RENAMED (bert) "Xbox Book.xtf" and (Snuffleupagus) "Xbox.xtf") with the originals, and remove or rename or ?just flat out MOVE to a user-created folder (like "Hacked Backups") the defualt.xbe file we got from the "Bert is cheating on
Ernie-_-Pheonix Release EvoX" exploit and reboot. Everything should be back to normal. I will elaborate if needed. Just post!

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FRAG'n O (Flashing Red And Green n Orange)
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This is completely NORMAL and TYPICAL of a EvoX / FreeX install (even with the Pheonix method). This is indicating that the Kernal is not lining up with your BIOS expectations and THUS indicating your BIOS is "corrupt" and 'needs service' ... If you have seen Error 21, you'll notice it's the only other Error that causes the lights on the front to Flash Red And Green n' Orange. So if you put two and two together, You're actually just saying "Oh fuck you already... just let me do what I want" to the X-Box (which is now so desperately trying to show you the Error 21 screen) but instead it has just given in like the red-headed step-child it is, and has given in to your sick whim.
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E: Applications/Games
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This is DEFINITELY possible. A lot of people have been asking if it is indeed possible to do this, and it is as far as I have tried. I have Halo on my E:games folder and DVDX 2.0 on my E:apps folder and BOTH work fine (without any reboots btw).
So basically, this should work without a hitch. Just remember to edit your EvoX.ini file appropriately to point to the correct drive path (i.e. E:apps)
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Linux issues
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Wellp, I have to say... I don't know why there are a few questions regarding Complex !loader here... honestly I don't mind them... but this thread is NOT to be based off of a Linux install. In fact, I didn't even use it. I used SOLELY the files found in the first two items in the tutorial (both which do not have anythingto do with Linux technically...)
But... Linux... well the thing is... if you are using the files I listed to use... linux shouldn't load. So, as much as it SUCKS you can't get it to load... this is actually GOOD because following my tutorial won't allow Linux to boot. So if you can;t, then you have done something right! Hoorah afterall! But seriously, stray from Linux on this one. It isn't needed, and will only provide more of a headache as it's one more hting to maintain. If you want more elaboration, I will comply as I'm interested in seeing what you all have to say in regards to this... but honestly, this tutorial is NOT meant to be used with Linux or Complex !loader.
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Kernal Versions
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Currently, only the following Kernals work (will add more as they appear):
4034
Hah.. pretty small list. Again, at work. Will update once I research more.
Keep in mind, this is an exploit designed around the ORIGINAL KERNAL (4034). That's what I lucked out on with mine, and that's why I haven't posed any questions. I am completely content with my X-Box now, save for the fact it doesn't allow me full access to F:... I believe this is a bug however, as it is stated in the Pheonix release to have allowed usage of the F: drive. I could be wrong. More to come!
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Thanks for all the kind complments. I do appreciate them. It isn't my FIRST tutorial, and I have actually been doing this stuff since the Dreamcast days. This is just my first attempt on X-Box software hacking. Hardware hacking I've been in on for a while, but not too much experience.
I will definitely keep updating my posts and such. This is my baby

Thanks again! Hope this helps.