Comment 2 for bug 1550726

With apt-utils 1.2.4, the behavior has changed: 5 packages are not even listed in Packages anymore, including nemo_2.8.6-11_amd64.deb package:

Here, 24 packages are located in the folder:

Ubuntu/dists/wily/system-tools/binary-amd64# ll *.deb
-rw-r--r-- 1 root root 1116256 Mar 5 12:19 apt_1.2.4_amd64.deb
-rw-r--r-- 1 root root 342418 Mar 5 12:19 apt-doc_1.2.4_all.deb
-rw-r--r-- 1 root root 151352 Mar 5 12:19 apt-transport-https_1.2.4_amd64.deb
-rw-r--r-- 1 root root 387240 Mar 5 12:19 apt-utils_1.2.4_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 12244162 Feb 28 16:02 gimp_2.9.2-11_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 3663042 Feb 23 11:21 git_2.6.0-11_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 3647806 Feb 23 11:21 git_2.6.3-11_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 3684722 Feb 28 12:03 git_2.7.2-11_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 1646294 Feb 23 11:21 gparted_0.24.0-11_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 1653508 Feb 28 15:32 gparted_0.25.0-11_amd64.deb
-rw-r--r-- 1 root root 180902 Mar 5 12:19 libapt-inst2.0_1.2.4_amd64.deb
-rw-r--r-- 1 root root 813750 Mar 5 12:19 libapt-pkg5.0_1.2.4_amd64.deb
-rw-r--r-- 1 root root 221594 Mar 5 12:19 libapt-pkg-dev_1.2.4_amd64.deb
-rw-r--r-- 1 root root 994680 Mar 5 12:20 libapt-pkg-doc_1.2.4_all.deb
-rw-r--r-- 1 actionmystique actionmystique 408538 Feb 28 14:21 libbabl-0.1-0_0.1.16-11_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 21538808 Feb 28 14:00 libgegl-0.3-0_0.3.4-11_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 1072388 Mar 5 12:46 nemo_2.8.6-11_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 25388 Feb 23 11:21 nemo-fileroller_2.8.1-11_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 129268 Feb 23 11:21 nemo-gtkhash_0.7.0-11_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 779684 Mar 2 11:45 realtek-wifi-drivers_4.2.6-10_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 781530 Feb 23 11:21 realtek-wifi-drivers_4.2-rc1-10_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 533770 Feb 23 11:21 redis-server_3.0.4-10_amd64.deb
-rw-r--r-- 1 actionmystique actionmystique 538628 Feb 23 11:21 redis-server_3.0.7-10_amd64.deb
-rw-rw-r-- 1 actionmystique actionmystique 1071418 Feb 23 11:21 xca_1.3.2-10_amd64.deb

Only 19 packages are described in Packages (cf. attached file).
I have also uploaded the config file I use for apt-ftparchive.

I can't find what the 5 missing packages have in common to explain this issue.