לזכות ידידי האהוב ר' צבי משה בן איתן אברהם הלוי וכל בני ביתו
The gemara in Sanhedrin says that when Bar Kochba claimed he was Moshiach they tested whether he could judge using his sense of smell [מורח ודאין] which is the quality of Moshiach. When they saw that he could not - they killed him [as a false Messiah]. The Rambam [Melachim 11/3] writes that Rebbe Akiva and the other sages thought that Bar Kochba was Moshiach but ultimately he was killed due to sins [the Rambam doesn't tell us whose sins]. The Raavad jumps in and says to the Rambam - "WAIT! What about the gemara that teaches that he wasn't able to smell and judge and that is why they killed him?? The Kesef Mishna answers that the Rambam was basing his version of the story on a Medrash in Eicha while the gemara in Sanhedrin which expects supernatural capabilities from Moshiach argues with Shmuel who says that there is no difference between this world and Moshiach's world besides our political freedom [אין בין עולם הזה לימות המשיח אלא שיעבוד מלכויות בלבד]. The Rambam ruled in accordance with Shmuel so he doesn't accept the version that his supernatural smelling ability was tested.
The explanation is as follows: How do we understand the notion of מורח ודאין - judging with the sense of smell? The gemara [R.H. 21b] says that Koheles wanted to judge with his heart, without witnesses or warnings and a heavenly voice came out and said "יושר דברי אמת - על פי שנים עדים יקום דבר" - In order to judge truthfully there have to be two witnesses and we may not rely on any supernatural intuition of the judge. So how can one judge by merely smelling without the accepted procedure of listening to testimony from witnesses etc.?
Perhaps the Rambam learned that the gemara in Rosh Hashana was following Shmuel that when Moshiach comes there will be nothing supernatural and the Torah will be kept in its classical form. For as long as we live in our world without any drastic changes in reality, we follow the ancient rules. If so, it also makes sense that we don't allow one to judge without witnesses, as the gemara says. The gemara in Sanhedrin that talks about מורח ודאין takes the approach that we MAY judge without the classical procedure of witnesses etc.
That would also explain what the Rambam meant when he said in the halacha where he spoke about Bar Kochba [Melachim 11/3] that the Torah is eternal etc. He was alluding to the fact that we rule like the pasuk יושר דברי אמת and the court procedure remains constant and we don't require מורח ודאין.
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