When running repack while doing repo writes, `packfile_load__cb()` can see some temporary files in the directory that are bigger than the usual, and makes `memcmp` overflow on the `p->pack_name` string. ASAN detected this. This just uses `strncmp`, that should not have any performance impact and is safe for comparing strings of different sizes.

```
ERROR: AddressSanitizer: heap-buffer-overflow on address 0x61200001a3f3 at pc 0x7f4a9e1976ec bp 0x7ffc1f80e100 sp 0x7ffc1f80d8b0
READ of size 89 at 0x61200001a3f3 thread T0
SCARINESS: 26 (multi-byte-read-heap-buffer-overflow)
    #0 0x7f4a9e1976eb in __interceptor_memcmp.part.78 (/build/cfgr-admin#link-tree/libtools_build_sanitizers_asan-ubsan-py.so+0xcf6eb)
    #1 0x7f4a518c5431 in packfile_load__cb /build/libgit2/0.27.0/src/libgit2-0.27.0/src/odb_pack.c:213
    #2 0x7f4a518d9582 in git_path_direach /build/libgit2/0.27.0/src/libgit2-0.27.0/src/path.c:1134
    #3 0x7f4a518c58ad in pack_backend__refresh /build/libgit2/0.27.0/src/libgit2-0.27.0/src/odb_pack.c:347
    #4 0x7f4a518c1b12 in git_odb_refresh /build/libgit2/0.27.0/src/libgit2-0.27.0/src/odb.c:1511
    #5 0x7f4a518bff5f in git_odb__freshen /build/libgit2/0.27.0/src/libgit2-0.27.0/src/odb.c:752
    #6 0x7f4a518c17d4 in git_odb_stream_finalize_write /build/libgit2/0.27.0/src/libgit2-0.27.0/src/odb.c:1415
    #7 0x7f4a51b9d015 in Repository_write /build/pygit2/0.27.0/src/pygit2-0.27.0/src/repository.c:509
```

We strive to keep an options structure to many functions to be able to
extend options in the future without breaking the API. `git_indexer_new`
doesn't have one right now, but we want to be able to add an option
for enabling strict packfile verification.

Add a new `git_indexer_options` structure and adjust callers to use
that.

Next to including several files, our "common.h" header also declares
various macros which are then used throughout the project. As such, we
have to make sure to always include this file first in all
implementation files. Otherwise, we might encounter problems or even
silent behavioural differences due to macros or defines not being
defined as they should be. So in fact, our header and implementation
files should make sure to always include "common.h" first.

This commit does so by establishing a common include pattern. Header
files inside of "src" will now always include "common.h" as its first
other file, separated by a newline from all the other includes to make
it stand out as special. There are two cases for the implementation
files. If they do have a matching header file, they will always include
this one first, leading to "common.h" being transitively included as
first file. If they do not have a matching header file, they instead
include "common.h" as first file themselves.

This fixes the outlined problems and will become our standard practice
for header and source files inside of the "src/" from now on.

The `pack_entry_find_prefix` function receives a `git_rawobj` structure
as argument. While the function first initializes the structure to a
sensible state, Coverity is unable to correctly detect this, resulting
in a warning.

Fix this warning by initializing the object to all-zeroes before passing
it to the function.

Since writing multiple objects may all already exist in a single
packfile, avoid freshening that packfile repeatedly in a tight loop.
Instead, only freshen pack files every 2 seconds.

When writing an object, we calculate its OID and see if it exists in the
object database.  If it does, we need to freshen the file that contains
it.

Move the delta application functions into `delta.c`, next to the
similar delta creation functions.  Make the `git__delta_apply`
functions adhere to other naming and parameter style within the
library.