The most common and most likely answer to this crossword clue is the 5 letter word CODEX
I've seen this crossword clue in The Guardian
C
O
D
E
X
More clues leading to the result CODEX
Buddy explains!

The straight part
We know that "old manuscript" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case old manuscript = codex.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does CODEX mean?
CODEX noun- An early manuscript book.
- A book bound in the modern manner, by joining pages, as opposed to a rolled scroll.
- An official list of medicines and medicinal ingredients.