Include conflicts in `git_index_read_index`

Ensure that we include conflicts when calling `git_index_read_index`,
which will remove conflicts in the index that do not exist in the new
target, and will add conflicts from the new target.

Most of `git_index_read_index` is common to reading any iterator.
Refactor it out in case we want to implement `read_tree` in terms of it
in the future.

submodule: Try to fetch when update fails to find the target commit.

blame: increment reference count for origin's commit

When we create a blame origin, we try to look up the blob that is
to be blamed at a certain revision. When this lookup fails, e.g.
because the file did not exist at that certain revision, we fail
to create the blame origin and return `NULL`. The blame origin
that we have just allocated is thereby free'd with
`origin_decref`.

The `origin_decref` function does not only decrement reference
counts for the blame origin, though, but also for its commit and
blob. When this is done in the error case, we will cause an
uneven reference count for these objects. This may result in
hard-to-debug failures at seemingly unrelated code paths, where
we try to access these objects when they in fact have already
been free'd.

Fix the issue by refactoring `make_origin` such that we only
allocate the object after the only function that may fail so that
we do not have to call `origin_decref` at all. Also fix the
`pass_blame` function, which indirectly calls `make_origin`, to
free the commit when `make_origin` failed.

Reading patch files

Improve the README

When showing copy information because we are duplicating contents,
for example, when performing a `diff --find-copies-harder -M100 -B100`,
then show copy from/to lines in a patch, and do not show context.
Ensure that we can also parse such patches.

Patches may have no hunks when there's no modifications (for example,
in a rename).  Handle them.

Test that we can create a diff file, then parse the results and
that the two are identical in-memory.

Cleanups

cmake: do not use -fPIC for MSYS2

Avoid declaring old-style functions without any parameters.
Functions not accepting any parameters should be declared with
`void fn(void)`. See ISO C89 $3.5.4.3.

The MSYS2 build system automatically compiles all code with position-independent
code. When we manually add the -fPIC flag to the compiler flags, MSYS2 will
loudly complain about PIC being the default and thus not required.

Fix the annoyance by stripping -fPIC in MSYS2 enviroments like it is already
done for MinGW.

Thread namespacing

Drop node-gitteh.  Replace outdated PowerShell bindings with PSGit.

Indicate that if you make changes to libgit2 that you must distribute
the source _to libgit2_, not the source _of your program_.

The old pthread-file did re-implement the pthreads API with exact symbol
matching. As the thread-abstraction has now been split up between Unix- and
Windows-specific files within the `git_` namespace to avoid symbol-clashes
between libgit2 and pthreads, the rewritten wrappers have nothing to do with
pthreads anymore.

Rename the Windows-specific pthread-files to honor this change.

The function pthread_num_processors_np is currently unused and superseded by the
function `git_online_cpus`. Remove the function.

Fix truncation of SHA in error message for git_odb_read

HTTP authentication scheme name is case insensitive.

checkout: use empty baseline when no index file exists

documentation: improve docs for `checkout_head`

When no index file exists and a baseline is not explicitly provided, use
an empty baseline instead of trying to load `HEAD`.