The gemara has a machlokes between R' Meir and R' Yehuda whether the sefer torah that was written by moshe was actually in the Aron with the luchos, or whether it was in the kodesh hakadashim on the side of the Aron. The gemara (14b) refers to this sefer torah as the ספר עזרה. Why would the sefer torah that is kept inside the kodesh hakadashim be called the sefer of the Azara - courtyard? Rashi is apparently bothered by this question and says that the sefer that Moshe Rabbeinu wrote was read from by the king during hakhel, and by the kohen gadol on yom kippur. Apparently rashi held that it was permitted to go into the kodesh hakadashim to take out the torah in order to read it.
Tosafos 14a asks why the gemara finds it necessary to leave some space in the Aron so that the sefer torah can be put in and removed easily, it was never removed since it is forbidden to enter the kodesh kadashim except on yom kippur, and we don't find any mention in the mishnayos of yom kippur that they would use this sefer torah? Tosafos clearly assumes not like rashi and holds that this sefer wasn't used, and is therefore troubled by why they had to leave space to get it in and out easily. Tosafos answers that although it was never used they would sometimes remove it in order to repair it (and one may enter the kodesh hakadashim in order to fix it, so too one may enter to fix the sefer torah). Also, between the destruction of mishkan shiloh and the second beis hamikdash, they would use the torah. The Rashash suggests that even rashi agrees with Tosafos that one may not enter the kodesh hakadashim to remove the sefer torah, but during the second mikdash when there wasn't any Aron it was used (that is why it is called the sefer azara - perhaps during that time it was actually kept in the azara).