This is the simplest case I could come up with where git clone produced a initially modified state. Any ideas why this is happening? Is this another manifestation of crlf problems? --Beman D:\modular-boost\libs\intrusive>git clone --recursive git@github.com:boostorg/boost.git modular-boost ... much output, no apparent error messages... D:\modular-boost>git status # On branch master # Changes not staged for commit: # (use "git add <file>..." to update what will be committed) # (use "git checkout -- <file>..." to discard changes in working directory) # (commit or discard the untracked or modified content in submodules) # # modified: libs/interprocess (modified content) # modified: libs/intrusive (modified content) # modified: libs/pool (modified content) # no changes added to commit (use "git add" and/or "git commit -a") D:\modular-boost>cd libs/pool D:\modular-boost\libs\pool>git status # Not currently on any branch. # Changes not staged for commit: # (use "git add <file>..." to update what will be committed) # (use "git checkout -- <file>..." to discard changes in working directory) # # modified: doc/images/mb1.svg # modified: doc/images/mb2.svg # modified: doc/images/mb3.svg # modified: doc/images/mb4.svg # modified: doc/images/pc1.svg # modified: doc/images/pc2.svg # modified: doc/images/pc3.svg # modified: doc/images/pc4.svg # modified: doc/images/pc5.svg # no changes added to commit (use "git add" and/or "git commit -a") D:\modular-boost\libs\pool>cd ..\interprocess D:\modular-boost\libs\interprocess>git status # Not currently on any branch. # Changes not staged for commit: # (use "git add <file>..." to update what will be committed) # (use "git checkout -- <file>..." to discard changes in working directory) # # modified: proj/vc7ide/managed_shared_memory.vcproj # modified: proj/vc7ide/offset_ptr_test.vcproj # no changes added to commit (use "git add" and/or "git commit -a") D:\modular-boost\libs\interprocess>cd ..\intrusive D:\modular-boost\libs\intrusive>git status # Not currently on any branch. # Changes not staged for commit: # (use "git add <file>..." to update what will be committed) # (use "git checkout -- <file>..." to discard changes in working directory) # # modified: proj/vc7ide/avl_multiset/avl_multiset.vcproj # modified: proj/vc7ide/avl_set/avl_set.vcproj # modified: proj/vc7ide/sg_multiset/sg_multiset.vcproj # modified: proj/vc7ide/sg_set/sg_set.vcproj # modified: proj/vc7ide/splay_multiset/splay_multiset.vcproj # modified: proj/vc7ide/splay_set/splay_set.vcproj # no changes added to commit (use "git add" and/or "git commit -a")