, если эти M1 и M2 всегда в полях 3 и 5, вы можете попробовать это
awk -F"," 'FNR==NR{
split($3,b," ")
split($5,c," ")
a[$1]=b[1]" "c[1]
next
}
($1 in a){
print "found: " $1" "a[$1]
}' file2.txt file1.txt
выход
# cat file2.txt
build.xml,/home/build/NUOP/project1,M1 eesX.java,/home/build/adm/acl,M2 ddexse3.htm,/home/class/adm/33eFg
filename, blah,M1 blah, blah, M2 blah , end
$ cat file1.txt
build.xml,/home/build/NUOP/project1 eesX.java,/home/build/adm/acl
$ ./shell.sh
found: build.xml M1 M2