fix use new run marker

[tejal29]

Fixes #1317, #1316

usually, during Run command temporary files get created and then get deleted later.
During that time, walk might encounter such a file and os.Stat may return err which would abort to the whole filesystem walk. due to this, Run command changed files is incomplete.
Instead of erroring out, print a warning to the user.

update-alternatives: using /usr/share/postgresql/11/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode
Setting up postgresql-client (11+200+deb10u3) ...
Processing triggers for libc-bin (2.28-10) ...
WARN[0160] error retrieving stat for file /etc/alternatives/pager.1.gz: stat /etc/alternatives/pager.1.gz: no such file or directory 
WARN[0160] error retrieving stat for file /etc/alternatives/rmt.8.gz: stat /etc/alternatives/rmt.8.gz: no such file or directory 
WARN[0160] error retrieving stat for file /etc/alternatives/awk.1.gz: stat /etc/alternatives/awk.1.gz: no such file or directory 
WARN[0160] error retrieving stat for file /etc/alternatives/nawk.1.gz: stat /etc/alternatives/nawk.1.gz: no such file or directory 
WARN[0160] error retrieving stat for file /etc/alternatives/builtins.7.gz: stat /etc/alternatives/builtins.7.gz: no such file or directory 
INFO[0160] Taking snapshot of files...