- Entering recovery is different than booting into the bootloader. When you see the reclining android with red exclamation point, you hold in the POWER button, then touch the VOL UP button. This takes you into Recovery. From here you can factory reset it, reboot into bootloader, reboot normally.
- I've had the endless boot animation problem before, it's hard to tell if an application's data is causing the issue, or an app itself. I don't believe there's a way to boot into Safe Mode from bootloader. I'm afraid your arguably easiest fix is to factory reset it and configure it again.
If you're going to reset it, you might consider unlocking it in Bootloader. Performing the unlock wipes user data as a security precaution, which would happen if you factory reset it. Once unlocked, you can install a custom Recovery, e.g. Team Win aka TWRP or ClockworkMod aka CWM. Custom recovery modules give ou options like doing full backups, restores, sideloading updates, and (if you're so inclined) rooting the device. THIS is the benefit of having a Nexus phone, they are designed for enthusiasts and developers.
Instructions for unlocking and rooting can be found on various Android sites. One of the best tutorials is on Androidcentral.com IMHO. You will need to install and use the Android SDK tools on your computer, though there are some third party utilities that make it easier.
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