Remove the present-despite-SKIP_WORKTREE class of bugs (for sparse-checkouts)

(Maintainer note: This series builds on (v2 of) vd/sparse-clean-etc, because it tweaks one of the testcases added there.)

(Note 2: There was a previous RFC round of this series at
https://lore.kernel.org/git/[email protected]/.)

Files in the present-despite-SKIP_WORKTREE state have caused no ends of discussions and bugs[1,2,3,4,5,6,...and lots of others]. Trying to address the big issue of discovering & recovering from this state has befuddled me for over a year because I was worried we'd need additional code at every skip_worktree-checking path in the code (and they are all over the place), and that we'd make the code significantly slower unless we plumbed a bunch of additional information all over the place to allow some reasonable optimizations.

This series tries to solve the problem a bit differently by automatic early discovery and recovery; as a result, it greatly simplifies the landscape, reduces our testing matrix burden, and fixes a large swath of bugs. And I figured out how to get the perf cost down to essentially negligible.

Changes since v1 (or v2 if you count RFC as v1):

* now includes some fixes for testcases from ds/fetch-pull-with-sparse-index (which topic marked its own new tests as potentially suboptimal; with my series, the sparse behavior now matches the full tree behavior on that test. Wahoo!). Note that Junio's version of vd/sparse-clean-etc already includes ds/fetch-pull-with-sparse-index, so no need to merge in anything extra.

Changes since RFC version:

* updated the commit messages as per suggestions from Victoria, including adding performance measurements
* renamed the new function to use a clearer name
* replaced the final patch with a different optimization, which is both simpler and performs quite a bit better (the cost for my previous patch 5 was already decent in many cases, but had a few cases where the cost was significant).

Quick overview:

* Patches 1 & 2 add a test to demonstrate accidental deletion of possibly-modified files, and then fix the bug.
* Patch 3 is the crux of this series; a small amount of code with a huge commit message
* Patch 4 updates the documentation
* Patch 5 adds an optimization to reduce the performance impact of patch 3

[1]
https://lore.kernel.org/git/CABPp-BFnFpzwGC11TLoLs8YK5yiisA5D5-fFjXnJsbESVDwZsA@mail.gmail.com/
[2]
https://lore.kernel.org/git/CABPp-BGJ_Nvi5TmgriD9Bh6eNXE2EDq2f8e8QKXAeYG3BxZafA@mail.gmail.com/
[3]
https://lore.kernel.org/git/[email protected]/
[4] commit 66b209b ("merge-ort: implement CE_SKIP_WORKTREE handling with conflicted entries", 2021-03-20) [5] commit ba359fd ("stash: fix stash application in sparse-checkouts", 2020-12-01) [6]
https://lore.kernel.org/git/CABPp-BH9tju7WVm=QZDOvaMDdZbpNXrVWQdN-jmfN8wC6YVhmw@mail.gmail.com/

Elijah Newren (5):
t1011: add testcase demonstrating accidental loss of user
modifications
unpack-trees: fix accidental loss of user changes
repo_read_index: clear SKIP_WORKTREE bit from files present in
worktree
Update documentation related to sparsity and the skip-worktree bit Accelerate clear_skip_worktree_from_present_files() by caching

 Documentation/git-read-tree.txt          | 12 +++-
 Documentation/git-sparse-checkout.txt    | 76 ++++++++++++++----------
 Documentation/git-update-index.txt       | 57 +++++++++++++-----
 repository.c                             |  7 +++
 sparse-index.c                           | 73 +++++++++++++++++++++++
 sparse-index.h                           |  1 +
 t/t1011-read-tree-sparse-checkout.sh     | 23 ++++++-
 t/t1092-sparse-checkout-compatibility.sh | 41 ++++++-------
 t/t3705-add-sparse-checkout.sh           |  2 +
 t/t6428-merge-conflicts-sparse.sh        | 23 ++-----
 t/t7012-skip-worktree-writing.sh         | 44 +++-----------
 t/t7817-grep-sparse-checkout.sh          | 11 +++-
 unpack-trees.c                           |  4 +-
 13 files changed, 246 insertions(+), 128 deletions(-)

base-commit: 48609de3bf32befb69c40c1a2595a98dac0448b4
Published-As: https://github.com/gitgitgadget/git/releases/tag/pr-1114%2Fnewren%2Ffix-present-despite-skip-worktree-v2
Fetch-It-Via: git fetch https://github.com/gitgitgadget/git pr-1114/newren/fix-present-despite-skip-worktree-v2
Pull-Request: https://github.com/gitgitgadget/git/pull/1114

Range-diff vs v1:

 1:  c553d558c2f = 1:  d50d804af4e t1011: add testcase demonstrating accidental loss of user modifications
 2:  1e3958576e2 = 2:  206c638fa90 unpack-trees: fix accidental loss of user changes
 3:  b263cc75b7d ! 3:  11d46a399d2 repo_read_index: clear SKIP_WORKTREE bit from files present in worktree

@@ t/t1092-sparse-checkout-compatibility.sh: test_expect_success 'update-index modi

# When skip-worktree is disabled (even on files outside sparse cone), file # is updated in the index
+@@ t/t1092-sparse-checkout-compatibility.sh: test_expect_success 'ls-files' '
+ test_cmp dense sparse &&
+
+ # Set up a strange condition of having a file edit
+- # outside of the sparse-checkout cone. This is just
+- # to verify that sparse-checkout and sparse-index
+- # behave the same in this case.
++ # outside of the sparse-checkout cone. We want to verify
++ # that all modes handle this the same, and detect the
++ # modification.
+ write_script edit-content <<-\EOF &&
+- mkdir folder1 &&
++ mkdir -p folder1 &&
+ echo content >>folder1/a
+ EOF
+- run_on_sparse ../edit-content &&
++ run_on_all ../edit-content &&
+
+- # ls-files does not currently notice modified files whose
+- # cache entries are marked SKIP_WORKTREE. This may change
+- # in the future, but here we test that sparse index does
+- # not accidentally create a change of behavior.
+- test_sparse_match git ls-files --modified &&
+- test_must_be_empty sparse-checkout-out &&
+- test_must_be_empty sparse-index-out &&
++ test_all_match git ls-files --modified &&
+
+ git -C sparse-index ls-files --sparse --modified >sparse-index-out &&
+- test_must_be_empty sparse-index-out &&
++ cat >expect <<-\EOF &&
++ folder1/a
++ EOF
++ test_cmp expect sparse-index-out &&
+
+ # Add folder1 to the sparse-checkout cone and
+ # check that ls-files shows the expanded files.
+ test_sparse_match git sparse-checkout add folder1 &&
+- test_sparse_match git ls-files --modified &&
++ test_all_match git ls-files --modified &&
+
+ test_all_match git ls-files &&
+ git -C sparse-index ls-files --sparse >actual &&

## t/t3705-add-sparse-checkout.sh ##
@@ t/t3705-add-sparse-checkout.sh: setup_sparse_entry () {

 4:  c74ad19616e = 4:  0af00779128 Update documentation related to sparsity and the skip-worktree bit
 5:  e68028ebe0a = 5:  05ac964e630 Accelerate clear_skip_worktree_from_present_files() by caching

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