Mom and Dad are going out for the evening and they give their son instructions throughout the day. At 10:00 AM, they tell Junior, “No parties.” At noon, they say, “Don’t open the door for strangers.” At 4:00 PM, they say, “Lights out at midnight.” When they leave, they say, “Do everything we told you.” How many rules did Mom and Dad give Junior? Three: no parties, don’t open the door for strangers and lights out at midnight. “Do everything we told you” is not a separate agenda item.
A mitzvah is a command to do something (to eat matzah on Seder night, to blow shofar on Rosh Hashana, etc.) or not to do something (not to wear garments containing shaatnez, not to marry one’s own stepmother, etc.). A mitzvah by definition has a specific referent. A general command to do as we’ve been instructed is not in and of itself one of the 613 mitzvos.
The Torah commands us many times to follow the mitzvos or not to stray from what God has commanded. The Rambam provides a number of examples, such as “everything I have told you, you must observe” (Exodus 23:13) and “you shall keep My statutes” (Leviticus 19:19).
As with the other principles, the Rambam indicates that some earlier compilers made mistakes and included general commands in their counts. Specifically, they have counted the opening phrase of parshas Kedoshim, “You shall be holy” (Leviticus 19:2). This is not a mitzvah in and of itself, the Rambam says, but rather a reminder to keep the mitzvos. How are we to make ourselves holy? By separating ourselves from everything about which God has warned us. Rambam quotes a number of supports to this position, including a statement from the Sifre that explicitly states that “you shall be holy” refers to the holiness of the mitzvos.
And so, the commandment to be holy is not itself a mitzvah. Like commands to keep all the laws or not to rebel, it is a catch-all category that includes the mitzvos as a whole. It is not counted separately in addition to them as it requires no particular action of its own.