Merge pull request git-for-windows#156: Incremental commit-graph files

This PR matches the commits that Junio is tracking from [this patch series](https://public-inbox.org/git/[email protected]/).
The only commit required that is extra is a merge between `vfs-2.22.0`
and `ds/commit-graph-incremental` because we took `ds/close-object-store`
a bit earlier (we needed it). Also, there was a small conflict in `packfile.[c|h]`
related to `ds/multi-pack-index-expire`.

Here is a copy of the cover letter for that series:

The commit-graph is a valuable performance feature for repos with large
commit histories, but suffers from the same problem as git repack: it
rewrites the entire file every time. This can be slow when there are
millions of commits, especially after we stopped reading from the
commit-graph file during a write in 43d3561 (commit-graph write: don't die
if the existing graph is corrupt).

Instead, create a "chain" of commit-graphs in the
.git/objects/info/commit-graphs folder with name graph-{hash}.graph. The
list of hashes is given by the commit-graph-chain file, and also in a "base
graph chunk" in the commit-graph format. As we read a chain, we can verify
that the hashes match the trailing hash of each commit-graph we read along
the way and each hash below a level is expected by that graph file.

When writing, we don't always want to add a new level to the stack. This
would eventually result in performance degradation, especially when
searching for a commit (before we know its graph position). We decide to
merge levels of the stack when the new commits we will write is less than
half of the commits in the level above. This can be tweaked by the
`--size-multiple` and `--max-commits` options.

The performance is necessarily amortized across multiple writes, so I tested
by writing commit-graphs from the (non-rc) tags in the Linux repo. My test
included 72 tags, and wrote everything reachable from the tag using 
`--stdin-commits`. Here are the overall perf numbers:

```
write --stdin-commits:         8m 12s
write --stdin-commits --split:    28s
write --split && verify --shallow: 60s
```

Author: derrickstolee

Documentation/git-commit-graph.txt

@@ -10,7 +10,7 @@ SYNOPSIS
 --------
 [verse]
 'git commit-graph read' [--object-dir <dir>]
-'git commit-graph verify' [--object-dir <dir>]
+'git commit-graph verify' [--object-dir <dir>] [--shallow]
 'git commit-graph write' <options> [--object-dir <dir>]
 
 
@@ -26,7 +26,7 @@ OPTIONS
 	Use given directory for the location of packfiles and commit-graph
 	file. This parameter exists to specify the location of an alternate
 	that only has the objects directory, not a full `.git` directory. The
-	commit-graph file is expected to be at `<dir>/info/commit-graph` and
+	commit-graph file is expected to be in the `<dir>/info` directory and
 	the packfiles are expected to be in `<dir>/pack`.
 
 
@@ -51,6 +51,25 @@ or `--stdin-packs`.)
 +
 With the `--append` option, include all commits that are present in the
 existing commit-graph file.
++
+With the `--split` option, write the commit-graph as a chain of multiple
+commit-graph files stored in `<dir>/info/commit-graphs`. The new commits
+not already in the commit-graph are added in a new "tip" file. This file
+is merged with the existing file if the following merge conditions are
+met:
++
+* If `--size-multiple=<X>` is not specified, let `X` equal 2. If the new
+tip file would have `N` commits and the previous tip has `M` commits and
+`X` times `N` is greater than  `M`, instead merge the two files into a
+single file.
++
+* If `--max-commits=<M>` is specified with `M` a positive integer, and the
+new tip file would have more than `M` commits, then instead merge the new
+tip with the previous tip.
++
+Finally, if `--expire-time=<datetime>` is not specified, let `datetime`
+be the current time. After writing the split commit-graph, delete all
+unused commit-graph whose modified times are older than `datetime`.
 
 'read'::
 
@@ -61,6 +80,9 @@ Used for debugging purposes.
 
 Read the commit-graph file and verify its contents against the object
 database. Used to check for corrupted data.
++
+With the `--shallow` option, only check the tip commit-graph file in
+a chain of split commit-graphs.
 
 
 EXAMPLES

Documentation/technical/commit-graph-format.txt

@@ -44,8 +44,9 @@ HEADER:
 
   1-byte number (C) of "chunks"
 
-  1-byte (reserved for later use)
-     Current clients should ignore this value.
+  1-byte number (B) of base commit-graphs
+      We infer the length (H*B) of the Base Graphs chunk
+      from this value.
 
 CHUNK LOOKUP:
 
@@ -92,6 +93,12 @@ CHUNK DATA:
       positions for the parents until reaching a value with the most-significant
       bit on. The other bits correspond to the position of the last parent.
 
+  Base Graphs List (ID: {'B', 'A', 'S', 'E'}) [Optional]
+      This list of H-byte hashes describe a set of B commit-graph files that
+      form a commit-graph chain. The graph position for the ith commit in this
+      file's OID Lookup chunk is equal to i plus the number of commits in all
+      base graphs.  If B is non-zero, this chunk must exist.
+
 TRAILER:
 
 	H-byte HASH-checksum of all of the above.

Documentation/technical/commit-graph.txt

@@ -127,22 +127,196 @@ Design Details
   helpful for these clones, anyway. The commit-graph will not be read or
   written when shallow commits are present.
 
-Future Work
------------
-
-- After computing and storing generation numbers, we must make graph
-  walks aware of generation numbers to gain the performance benefits they
-  enable. This will mostly be accomplished by swapping a commit-date-ordered
-  priority queue with one ordered by generation number. The following
-  operations are important candidates:
-
-    - 'log --topo-order'
-    - 'tag --merged'
-
-- A server could provide a commit-graph file as part of the network protocol
-  to avoid extra calculations by clients. This feature is only of benefit if
-  the user is willing to trust the file, because verifying the file is correct
-  is as hard as computing it from scratch.
+Commit Graphs Chains
+--------------------
+
+Typically, repos grow with near-constant velocity (commits per day). Over time,
+the number of commits added by a fetch operation is much smaller than the
+number of commits in the full history. By creating a "chain" of commit-graphs,
+we enable fast writes of new commit data without rewriting the entire commit
+history -- at least, most of the time.
+
+## File Layout
+
+A commit-graph chain uses multiple files, and we use a fixed naming convention
+to organize these files. Each commit-graph file has a name
+`$OBJDIR/info/commit-graphs/graph-{hash}.graph` where `{hash}` is the hex-
+valued hash stored in the footer of that file (which is a hash of the file's
+contents before that hash). For a chain of commit-graph files, a plain-text
+file at `$OBJDIR/info/commit-graphs/commit-graph-chain` contains the
+hashes for the files in order from "lowest" to "highest".
+
+For example, if the `commit-graph-chain` file contains the lines
+
+```
+	{hash0}
+	{hash1}
+	{hash2}
+```
+
+then the commit-graph chain looks like the following diagram:
+
+ +-----------------------+
+ |  graph-{hash2}.graph  |
+ +-----------------------+
+	  |
+ +-----------------------+
+ |                       |
+ |  graph-{hash1}.graph  |
+ |                       |
+ +-----------------------+
+	  |
+ +-----------------------+
+ |                       |
+ |                       |
+ |                       |
+ |  graph-{hash0}.graph  |
+ |                       |
+ |                       |
+ |                       |
+ +-----------------------+
+
+Let X0 be the number of commits in `graph-{hash0}.graph`, X1 be the number of
+commits in `graph-{hash1}.graph`, and X2 be the number of commits in
+`graph-{hash2}.graph`. If a commit appears in position i in `graph-{hash2}.graph`,
+then we interpret this as being the commit in position (X0 + X1 + i), and that
+will be used as its "graph position". The commits in `graph-{hash2}.graph` use these
+positions to refer to their parents, which may be in `graph-{hash1}.graph` or
+`graph-{hash0}.graph`. We can navigate to an arbitrary commit in position j by checking
+its containment in the intervals [0, X0), [X0, X0 + X1), [X0 + X1, X0 + X1 +
+X2).
+
+Each commit-graph file (except the base, `graph-{hash0}.graph`) contains data
+specifying the hashes of all files in the lower layers. In the above example,
+`graph-{hash1}.graph` contains `{hash0}` while `graph-{hash2}.graph` contains
+`{hash0}` and `{hash1}`.
+
+## Merging commit-graph files
+
+If we only added a new commit-graph file on every write, we would run into a
+linear search problem through many commit-graph files.  Instead, we use a merge
+strategy to decide when the stack should collapse some number of levels.
+
+The diagram below shows such a collapse. As a set of new commits are added, it
+is determined by the merge strategy that the files should collapse to
+`graph-{hash1}`. Thus, the new commits, the commits in `graph-{hash2}` and
+the commits in `graph-{hash1}` should be combined into a new `graph-{hash3}`
+file.
+
+			    +---------------------+
+			    |                     |
+			    |    (new commits)    |
+			    |                     |
+			    +---------------------+
+			    |                     |
+ +-----------------------+  +---------------------+
+ |  graph-{hash2} |->|                     |
+ +-----------------------+  +---------------------+
+	  |                 |                     |
+ +-----------------------+  +---------------------+
+ |                       |  |                     |
+ |  graph-{hash1} |->|                     |
+ |                       |  |                     |
+ +-----------------------+  +---------------------+
+	  |                  tmp_graphXXX
+ +-----------------------+
+ |                       |
+ |                       |
+ |                       |
+ |  graph-{hash0} |
+ |                       |
+ |                       |
+ |                       |
+ +-----------------------+
+
+During this process, the commits to write are combined, sorted and we write the
+contents to a temporary file, all while holding a `commit-graph-chain.lock`
+lock-file.  When the file is flushed, we rename it to `graph-{hash3}`
+according to the computed `{hash3}`. Finally, we write the new chain data to
+`commit-graph-chain.lock`:
+
+```
+	{hash3}
+	{hash0}
+```
+
+We then close the lock-file.
+
+## Merge Strategy
+
+When writing a set of commits that do not exist in the commit-graph stack of
+height N, we default to creating a new file at level N + 1. We then decide to
+merge with the Nth level if one of two conditions hold:
+
+  1. `--size-multiple=<X>` is specified or X = 2, and the number of commits in
+     level N is less than X times the number of commits in level N + 1.
+
+  2. `--max-commits=<C>` is specified with non-zero C and the number of commits
+     in level N + 1 is more than C commits.
+
+This decision cascades down the levels: when we merge a level we create a new
+set of commits that then compares to the next level.
+
+The first condition bounds the number of levels to be logarithmic in the total
+number of commits.  The second condition bounds the total number of commits in
+a `graph-{hashN}` file and not in the `commit-graph` file, preventing
+significant performance issues when the stack merges and another process only
+partially reads the previous stack.
+
+The merge strategy values (2 for the size multiple, 64,000 for the maximum
+number of commits) could be extracted into config settings for full
+flexibility.
+
+## Deleting graph-{hash} files
+
+After a new tip file is written, some `graph-{hash}` files may no longer
+be part of a chain. It is important to remove these files from disk, eventually.
+The main reason to delay removal is that another process could read the
+`commit-graph-chain` file before it is rewritten, but then look for the
+`graph-{hash}` files after they are deleted.
+
+To allow holding old split commit-graphs for a while after they are unreferenced,
+we update the modified times of the files when they become unreferenced. Then,
+we scan the `$OBJDIR/info/commit-graphs/` directory for `graph-{hash}`
+files whose modified times are older than a given expiry window. This window
+defaults to zero, but can be changed using command-line arguments or a config
+setting.
+
+## Chains across multiple object directories
+
+In a repo with alternates, we look for the `commit-graph-chain` file starting
+in the local object directory and then in each alternate. The first file that
+exists defines our chain. As we look for the `graph-{hash}` files for
+each `{hash}` in the chain file, we follow the same pattern for the host
+directories.
+
+This allows commit-graphs to be split across multiple forks in a fork network.
+The typical case is a large "base" repo with many smaller forks.
+
+As the base repo advances, it will likely update and merge its commit-graph
+chain more frequently than the forks. If a fork updates their commit-graph after
+the base repo, then it should "reparent" the commit-graph chain onto the new
+chain in the base repo. When reading each `graph-{hash}` file, we track
+the object directory containing it. During a write of a new commit-graph file,
+we check for any changes in the source object directory and read the
+`commit-graph-chain` file for that source and create a new file based on those
+files. During this "reparent" operation, we necessarily need to collapse all
+levels in the fork, as all of the files are invalid against the new base file.
+
+It is crucial to be careful when cleaning up "unreferenced" `graph-{hash}.graph`
+files in this scenario. It falls to the user to define the proper settings for
+their custom environment:
+
+ 1. When merging levels in the base repo, the unreferenced files may still be
+    referenced by chains from fork repos.
+
+ 2. The expiry time should be set to a length of time such that every fork has
+    time to recompute their commit-graph chain to "reparent" onto the new base
+    file(s).
+
+ 3. If the commit-graph chain is updated in the base, the fork will not have
+    access to the new chain until its chain is updated to reference those files.
+    (This may change in the future [5].)
 
 Related Links
 -------------
@@ -170,3 +344,7 @@ Related Links
 
 [4] https://public-inbox.org/git/[email protected]/T/#u
     A patch to remove the ahead-behind calculation from 'status'.
+
+[5] https://public-inbox.org/git/[email protected]/
+    A discussion of a "two-dimensional graph position" that can allow reading
+    multiple commit-graph chains at the same time.