modified annotations input in compare.py

outputs/compare/cha-chaaligned/cha-chaaligned.txt

@@ -1 +0,0 @@
-../../../.git/annex/objects/75/p6/MD5E-s78--1d64fbe4cd828528b846485f7f9b557a.txt/MD5E-s78--1d64fbe4cd828528b846485f7f9b557a.txt

outputs/compare/cha-eaf/cha-eaf.txt

@@ -1 +0,0 @@
-../../../.git/annex/objects/3p/25/MD5E-s79--7202fe4df840c7f196de3adc92974ed0.txt/MD5E-s79--7202fe4df840c7f196de3adc92974ed0.txt

outputs/compare/eaf-cha/eaf-cha.txt

@@ -0,0 +1 @@
+../../../.git/annex/objects/vx/2v/MD5E-s79--cb947e26a9d3b3bbbbfd8315ce6440ac.txt/MD5E-s79--cb947e26a9d3b3bbbbfd8315ce6440ac.txt

outputs/compare/eaf-chaaligned/eaf-chaaligned.txt

@@ -0,0 +1 @@
+../../../.git/annex/objects/1j/JW/MD5E-s80--ba2cd379ead8d6cc8b9f35c816eba9f2.txt/MD5E-s80--ba2cd379ead8d6cc8b9f35c816eba9f2.txt