Please check while file tracking:

$ pijul init p1
$ cd p1
$ pijul add -rf .
Tracked 1 path(s)
$ pijul ls
.ignore
$ pijul diff --short -u
A .ignore
$ rm .ignore
$ pijul diff --short -u
# EMPTY
# Question: maybe should be (must?) 'D .ignore' ?
#
$ pijul ls
.ignore
#
# so i have got tracked file without working dir
#
$ touch a
$ pijul add a
$ pijul rec -am"."
Hash: 2RE3GLJWFC5IQZHKWS2QMCVNUABWL33X6UVMIPUZBSJ7LYQ6E7MAC
$ pijul ls
.ignore
a
# still here
$ cd ..
$ pijul clone p1 p2
$ cd p2
$ pijul ls
a
# only one file
$