Recovered the most importatn of Ignacio's previous changes. Thanks to
treed3f6ad9cdcb4e8df1ba327592b1c4e5fc0d971a6
-rw-r--r-- 62 .gitignore
-rw-r--r-- 725 Fakefile
-rw-r--r-- 993 Makefile
-rw-r--r-- 1911 README
-rw-r--r-- 748 TODO
-rw-r--r-- 7264 Transform_Polynomial.java
-rw-r--r-- 1560 build.xml
drwxr-xr-x - bunwarpj
-rwxr-xr-x 170 c_sift_plugin
-rwxr-xr-x 338 c_vib
-rw-r--r-- 19 excludes
-rwxr-xr-x 42 grep
drwxr-xr-x - img
-rwxr-xr-x 97 info.sh
drwxr-xr-x - ini
-rwxr-xr-x 455 jar_it
-rwxr-xr-x 412 jdoc
drwxr-xr-x - lenscorrection
drwxr-xr-x - lineage
drwxr-xr-x - mpi
drwxr-xr-x - mpicbg
-rw-r--r-- 117 nit.trakem2
-rw-r--r-- 840 plugins.config
drwxr-xr-x - test
-rw-r--r-- 133 treeline-graph.trakem2
drwxr-xr-x - treeline