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auditd

auditd can be used to track for when a file is deleted, and provides some information about who or what process deleted that file. It can track other system or file changes as well.

Install the package:

apt install auditd

Using:

Set up an audit tracker (set 'foo' to some custom string):

auditctl -w /var/www/html/some_file -p wra -k foo

Search the logs for entries:

ausearch -k foo -i

Get some other general stats:

aureport -ts today -i -x --summary

Remove an audit tracker (notice the uppercase 'W'):

auditctl -W /var/www/html/some_file -p wra -k foo

Caveats:

Some reads and writes may not be tracked. It's complicated stuff, but check the -p option in man auditctl.