* Move keys to models/keys
* Rename models/keys -> models/asymkey
* change the missed package name
* Fix package alias
* Fix test
* Fix docs
* Fix test
* Fix test
* merge
* Some refactors related repository model
* Move more methods out of repository
* Move repository into models/repo
* Fix test
* Fix test
* some improvements
* Remove unnecessary function
* Fix a panic in NotifyCreateIssueComment (caused by string truncation)
* more unit tests
* refactor
* fix some edge cases
* use SplitStringAtByteN for comment content
The current implementation of checkBranchName is highly inefficient
involving opening the repository, the listing all of the branch names
checking them individually before then using using opened repo to get
the tags.
This PR avoids this by simply walking the references from show-ref
instead of opening the repository (in the nogogit case).
Signed-off-by: Andrew Thornton <art27@cantab.net>
* allways set a message-id on mails
* Add unit tests for mailer & Message-ID
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
* Refactor install page (db type)
* set correct default DB HOST for different DB TYPE
* remove legacy TiDB from documents
* unify the usage of DB TYPE, in code we only use "mysql". "MySQL" is only shown to users for friendly name.
* Gitea can use TiDB via MySQL protocol
Co-authored-by: zeripath <art27@cantab.net>
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
* Improve install code to avoid low-level mistakes.
If a user tries to do a re-install in a Gitea database, they gets a warning and double check.
When Gitea runs, it never create empty app.ini automatically.
Also some small (related) refactoring:
* Refactor db.InitEngine related logic make it more clean (especially for the install code)
* Move some i18n strings out from setting.go to make the setting.go can be easily maintained.
* Show errors in CLI code if an incorrect app.ini is used.
* APP_DATA_PATH is created when installing, and checked when starting (no empty directory is created any more).
This PR registers requests with the process manager and manages hierarchy within the processes.
Git repos are then associated with a context, (usually the request's context) - with sub commands using this context as their base context.
Signed-off-by: Andrew Thornton <art27@cantab.net>
This PR adds another option to app.ini make co-committed-by and co-authored-by trailers
optional on a per server basis.
Fix#17194
Signed-off-by: Andrew Thornton <art27@cantab.net>
Make relative unix sockets absolute by making them absolute against the AppWorkPath
Fix#17833
## ⚠️ BREAKING ⚠️
Prior to this PR relative unix sockets would have been asserted to be relative to the current working directory that gitea, gitea serv, hook and manager etc were running in. Hooks and Serv would have failed to work properly under this situation so we expect that although this is a technically breaking change the previous situation was already broken.
Signed-off-by: Andrew Thornton <art27@cantab.net>
MIME types can have multiple optional parameters, eg:
video/webm; codecs="w/e codec"; charset="binary"
This commit replaces the usage of regex for getting the "type/subtype"
with mime.ParseMediaType.
- Use the provided `doer` instead of `rel.Publisher`. The code will also
run on edited releases and deleted ones, which isn't necessary done by
`rel.Publisher`.
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
* More pleasantly handle broken or missing git repositories
In #17742 it was noted that there a completely invalid git repository underlying a
repo on gitea.com. This happened due to a problem during a migration however, it
is not beyond the realms of possibility that a corruption could occur to another
user.
This PR adds a check to RepoAssignment that will detect if a repository loading has
failed due to an absent git repository. It will then show a page suggesting the user
contacts the administrator or deletes the repository.
Fix#17742
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Update options/locale/locale_en-US.ini
Co-authored-by: techknowlogick <techknowlogick@gitea.io>
Co-authored-by: techknowlogick <techknowlogick@gitea.io>
* Remove unnecessary functions of User struct
* Move more database methods out of user struct
* Move more database methods out of user struct
* Fix template failure
* Fix bug
* Remove finished FIXME
* remove unnecessary code
Unfortunately due to a misread on my behalf I missed that git diff only learned
--skip-to in version 2.31.0. Thus this functionality was not working on older versions
of git.
This PR adds a handler that simply allows for us to skip reading the diffs until
we find the correct file to skip to.
Fix#17731
Signed-off-by: Andrew Thornton <art27@cantab.net>
Use hostmacher to replace matchlist.
And we introduce a better DialContext to do a full host/IP check, otherwise the attackers can still bypass the allow/block list by a 302 redirection.
- `.Teams` isn't a field on the User type, thus using the seperate
loaded teams.
- Add a space between `PathEscape` and argument.
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
This PR fixes the builtin avatar generator.
1. The random background color makes some images very dirty. So now we only use white background for avatars.
2. We use left-right mirror avatars to satisfy #14799
3. Fix a small padding error in the algorithm
* Add settings to allow different SMTP envelope from address
Sometimes it may be advisable to hide or alias the from address on an SMTP mail
envelope. This PR adds two new options to the mailer to allow setting of an overriding
from address.
Fix#17477
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Use a standalone struct name for Organization
* recover unnecessary change
* make the code readable
* Fix template failure
* Fix template failure
* Move HasMemberWithUserID to org
* Fix test
* Remove unnecessary user type check
* Fix test
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
* Prevent double sanitize.
* Use SanitizeReaderToWriter.
At the moment `actualRender` uses `SanitizeReader` to sanitize the output. But `SanitizeReader` gets called in `markup.render` too so the output gets sanitized twice.
I moved the `SanitizeReader` call into `RenderRaw` because this method does not use `markup.render`. I would like to remove the `RenderRaw`/`RenderRawString` methods too because they are only called from tests, the fuzzer and the `/markup/raw` api endpoint. This endpoint is not in use so I think we could remove them. If we really in the future need a method to render markdown without PostProcessing we could achieve this with a more flexible `renderer.NeedPostProcess` method.
* Prevent deadlock in TestPersistableChannelQueue
There is a potential deadlock in TestPersistableChannelQueue due to attempting to
shutdown the test queue before it is ready.
Signed-off-by: Andrew Thornton <art27@cantab.net>
* prevent npe
Signed-off-by: Andrew Thornton <art27@cantab.net>
Use check attribute code to check the assigned language of a file and send that in to
chroma as a hint for the language of the file.
Signed-off-by: Andrew Thornton <art27@cantab.net>
There are multiple places where Gitea does not properly escape URLs that it is building and there are multiple places where it builds urls when there is already a simpler function available to use this.
This is an extensive PR attempting to fix these issues.
1. The first commit in this PR looks through all href, src and links in the Gitea codebase and has attempted to catch all the places where there is potentially incomplete escaping.
2. Whilst doing this we will prefer to use functions that create URLs over recreating them by hand.
3. All uses of strings should be directly escaped - even if they are not currently expected to contain escaping characters. The main benefit to doing this will be that we can consider relaxing the constraints on user names and reponames in future.
4. The next commit looks at escaping in the wiki and re-considers the urls that are used there. Using the improved escaping here wiki files containing '/'. (This implementation will currently still place all of the wiki files the root directory of the repo but this would not be difficult to change.)
5. The title generation in feeds is now properly escaped.
6. EscapePound is no longer needed - urls should be PathEscaped / QueryEscaped as necessary but then re-escaped with Escape when creating html with locales Signed-off-by: Andrew Thornton <art27@cantab.net>
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Add copy button to markdown code blocks
Done mostly in JS because I think it's better not to try getting buttons
past the markup sanitizer.
* add svg module tests
* fix sanitizer regexp
* remove outdated comment
* vertically center button in issue comments as well
* add comment to css
* fix undefined on view file line copy
* combine animation less files
* Update modules/markup/markdown/markdown.go
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
* add test for different sizes
* add cloneNode and add tests for it
* use deep clone
* remove useless optional chaining
* remove the svg node cache
* unify clipboard copy string and i18n
* remove unused var
* remove unused localization
* minor css tweaks to the button
* comment tweak
* remove useless attribute
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
- Partialy resolvess #17596
- Resolves `badCall` errors from go-critic `badCall: suspicious Join on
1 argument`
- When only 1 argument is passed into `filepath.Join`, it won't do
anything special other than `filepath.Clean(...)` will be applied over
it.
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
Co-authored-by: 6543 <6543@obermui.de>
This PR adds [GitBucket](https://gitbucket.github.io/) as migration source.
Supported:
- Milestones
- Issues
- Pull Requests
- Comments
- Reviews
- Labels
There is no public usable instance so no integration tests added.
* Correctly handle failed migrations
There is a bug in handling failed migrations whereby the migration task gets decoupled
from the migration repository. This leads to a failure of the task to get deleted with
the repository and also leads to the migration failed page resulting in a ISE.
This PR removes the zeroing out of the task id from the migration but also makes
the migration handler tolerate missing tasks much nicer.
Fix#17571
Signed-off-by: Andrew Thornton <art27@cantab.net>
The functioning of the code indexer queue really only makes sense as an unique queue
and doing this allows use to simplify the indexer data to simply delete the data if
the repo is no longer in the db.
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Fixes#16558 CSV delimiter determiner
* Fixes#16558 - properly determine CSV delmiiter
* Moves quoteString to a new function
* Adds big test with lots of commas for tab delimited csv
* Adds comments
* Shortens the text of the test
* Removes single quotes from regexp as only double quotes need to be searched
* Fixes spelling
* Fixes check of length as it probalby will only be 1e4, not greater
* Makes sample size a const, properly removes truncated line
* Makes sample size a const, properly removes truncated line
* Fixes comment
* Fixes comment
* tests for FormatError() function
* Adds logic to find the limiter before or after a quoted value
* Simplifies regex
* Error tests
* Error tests
* Update modules/csv/csv.go
Co-authored-by: delvh <dev.lh@web.de>
* Update modules/csv/csv.go
Co-authored-by: delvh <dev.lh@web.de>
* Adds comments
* Update modules/csv/csv.go
Co-authored-by: delvh <dev.lh@web.de>
Co-authored-by: wxiaoguang <wxiaoguang@gmail.com>
Co-authored-by: zeripath <art27@cantab.net>
Co-authored-by: delvh <dev.lh@web.de>
There is a small bug in the way that repo access is checked in
repoAssignment: Accessibility is checked by checking if the user has a
marked access to the repository instead of checking if the user has any
team granted access.
This PR changes this permissions check to use HasAccess() which does the
correct test. There is also a fix in the release api ListReleases where
it should return draft releases if the user is a member of a team with
write access to the releases.
The PR also adds a testcase.
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Fixes#16559 - Do not trim leading spaces for tab delimited
* Adds back semicolon delimited test
* Fixes linting
* Adds nolint directive to test because uses strings starting with spaces
Co-authored-by: zeripath <art27@cantab.net>
closed#17378
Both errors from #17378 were caused by #15175.
Problem 1 (error with added file):
`ToUTF8WithFallbackReader` creates a `MultiReader` from a `byte[2048]` and the remaining reader. `CreateReaderAndGuessDelimiter` tries to read 10000 bytes from this reader but only gets 2048 because that's the first reader in the `MultiReader`. Then the `if size < 1e4` thinks the input is at EOF and just returns that.
Problem 2 (error with changed file):
The blob reader gets defer closed. That was fine because the old version reads the whole file into memory. Now with the streaming version the close needs to defer after the method.
The API convert.toUser function makes the incorrect assumption that full names could
be rendered as is without being escaped. It therefore runs the names through
markup.Sanitize which leads to a double escape of user full names. This
pr stops this.
Signed-off-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
We have the `AppState` module now, it can store app related data easily. We do not need to create separate tables for each feature.
So the update checker can use `AppState` instead of a one-row dedicate table.
And the code of update checker is moved from `models` to `modules`.
Gitea writes its own AppPath into git hook scripts. If Gitea's AppPath changes, then the git push will fail.
This PR:
* Introduce an AppState module, it can persist app states into database
* During GlobalInit, Gitea will check if the current AppPath is the same as last one. If they don't match, Gitea will sync git hooks.
* Refactor some code to make them more clear.
* Also, "Detect if gitea binary's name changed" #11341 is related, we call models.RewriteAllPublicKeys to update ssh authorized_keys file
* Offer rsa-sha2-512 and rsa-sha2-256 algorithms in internal SSH
There is a subtle bug in the SSH library x/crypto/ssh which makes the incorrect
assumption that the public key type is the same as the signature algorithm type.
This means that only ssh-rsa signatures are offered by default.
This PR adds a workaround around this problem.
Fix#17175
Signed-off-by: Andrew Thornton <art27@cantab.net>
* as per review
Signed-off-by: Andrew Thornton <art27@cantab.net>
Fixes#16837 if a column is deleted.
We were clobbering the columns that were added by looping through the aline (base) and then when bline (head) was looped through, it clobbered what was in the "cells" array that is show in the diff, and then left a nil cell because nothing was shifted.
This fix properly shifts the cells, and properly puts the b cell either at its location or after, according to what the aline placed in the cells.
This includes test, adding a new test function since adding/removing cells works best with three columns, not two, which results in 4 columns of the resulting cells because it has a deleted column and an added column. If you try this locally, you can try those cases and others, such as adding a column.
There was no need to do anything special for the rows when `aline == 0 || bline == 0` so that was removed. This allows the same code to be used for removed or added lines, with the bcell text always being the RightCell, acell text being the LeftCell.
I still added the patch zeripath gave at https://github.com/go-gitea/gitea/issues/16837#issuecomment-913007382 so that just in case for some reason a cell is nil (which shouldn't happen now) it doesn't throw a 500 error, so the user can at least view the raw diff.
Also fixes in the [view.go](https://github.com/go-gitea/gitea/pull/17018/files#diff-43a7f4747c7ba8bff888c9be11affaafd595fd55d27f3333840eb19df9fad393L521) file how if a CSV file is empty (either created empty or if you edit it and remove all contents) it throws a huge 500 error when you then save it (when you view the file). Since we allow creating, saving and pushing empty files, we shouldn't throw an error on an empty CSV file, but just show its empty contents. This doesn't happen if it is a Markdown file or other type of file that is empty.
EDIT: Now handled in the markup/csv renderer code
Convert the old mirror syncing queue to the more modern queue format.
Fix a bug in the from the repo-archive queue PR - the assumption was made that uniqueness could be enforced with by checking equality in a map in channel unique queues - however this only works for primitive types - which was the initial intention but is an imperfect. This is fixed by marshalling the data and placing the martialled data in the unique map instead.
The documentation is also updated to add information about the deprecated configuration values.
Signed-off-by: Andrew Thornton <art27@cantab.net>
There is a slight race in checking of a context deadline exceed in #16467
which leads to a 500 on the repository page.
The solution is to check the error coming back from `*LogNameStatusRepoParser.Next()`
and if it is the `ContextDeadlineExceeded` break from the loop.
Fix#17314
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Ensure that git daemon export ok is created for mirrors
There is an issue with #16508 where it appears that create repo requires that the
repo does not exist. This causes #17241 where an error is reported because of this.
This PR fixes this and also runs update-server-info for mirrors and generated repos.
Fix#17241
Signed-off-by: Andrew Thornton <art27@cantab.net>
core.protectNTFS protects NTFS from files which may be difficult to remove or interact
with using the win32 api, however, it also appears to prevent such files from
being entered into the git indexes - fundamentally causing breakages with PRs that
affect these files. However, deliberately setting this to false may cause security
issues due to the remain sparse checkout of files in the merge pipeline.
The only sensible option therefore is to provide an optional setting which admins
could set which would forcibly switch this off if they are affected by this issue.
Fix#17092
Signed-off-by: Andrew Thornton <art27@cantab.net>
It makes Admin's life easier to filter users by various status.
* introduce window.config.PageData to pass template data to javascript module and small refactor
move legacy window.ActivityTopAuthors to window.config.PageData.ActivityTopAuthors
make HTML structure more IDE-friendly in footer.tmpl and head.tmpl
remove incorrect <style class="list-search-style"></style> in head.tmpl
use log.Error instead of log.Critical in admin user search
* use LEFT JOIN instead of SubQuery when admin filters users by 2fa. revert non-en locale.
* use OptionalBool instead of status map
* refactor SearchUserOptions.toConds to SearchUserOptions.toSearchQueryBase
* add unit test for user search
* only allow admin to use filters to search users
- Update default branch if needed
- Update protected branch if needed
- Update all not merged pull request base branch name
- Rename git branch
- Record this rename work and auto redirect for old branch on ui
Signed-off-by: a1012112796 <1012112796@qq.com>
Co-authored-by: delvh <dev.lh@web.de>
One of the biggest reasons for slow repository browsing is that we wait
until last commit information has been generated for all files in the
repository.
This PR proposes deferring this generation to a new POST endpoint that
does the look up outside of the main page request.
Signed-off-by: Andrew Thornton <art27@cantab.net>
close#17181
* for all pull requests API return permissions of caller
* for all webhook return empty permissions
Signed-off-by: Danila Kryukov <pricly_yellow@dismail.de>
Co-authored-by: delvh <dev.lh@web.de>
Co-authored-by: 6543 <6543@obermui.de>
Why this refactor
The goal is to move most files from `models` package to `models.xxx` package. Many models depend on avatar model, so just move this first.
And the existing logic is not clear, there are too many function like `AvatarLink`, `RelAvatarLink`, `SizedRelAvatarLink`, `SizedAvatarLink`, `MakeFinalAvatarURL`, `HashedAvatarLink`, etc. This refactor make everything clear:
* user.AvatarLink()
* user.AvatarLinkWithSize(size)
* avatars.GenerateEmailAvatarFastLink(email, size)
* avatars.GenerateEmailAvatarFinalLink(email, size)
And many duplicated code are deleted in route handler, the handler and the model share the same avatar logic now.
Nodeinfo is a way to expose certain metadata about a server for use of discovery regarding functionality of its federation capabilities.
Two endpoints are required:
1. `/.well-known/nodeinfo` which informs client where it can find the location of the location of its metadata (including which version of the schema is used)
2. the endpoint which exposes the metadata in json format according to schema.
Notes:
* `openRegistrations` is a required field, but I propose to set to false as default in case someone writes a crawler to discover "open" gitea instances
* to limit data leakage I also propose to not include the `usage` field (note it is required so it should be included, but left as empty).
More info:
https://github.com/jhass/nodeinfohttps://github.com/jhass/nodeinfo/tree/main/schemas/2.1http://nodeinfo.diaspora.software/protocol.html
* Nicely handle missing user in collaborations
It is possible to have a collaboration in a repository which refers to a no-longer
existing user. This causes the repository transfer to fail with an unusual error.
This PR makes `repo.getCollaborators()` nicely handle the missing user by ghosting
the collaboration but also adds consistency check. It also adds an
Access consistency check.
Fix#17044
Signed-off-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: KN4CK3R <admin@oldschoolhack.me>
There was a serious issue with the `gitea dump` command in 1.14.3-1.14.6 which led to corruption of the `config` field of the `repo_unit` table.
This PR adds a doctor command to attempt to fix the broken repo_units. Users affected by #16961 should run:
```
gitea doctor --fix --run fix-broken-repo-units
```
Fix#16961
Signed-off-by: Andrew Thornton <art27@cantab.net>
Add a new default theme `auto`, which will automatically switch between
`gitea` (light) and `arc-green` (dark) themes depending on the user's
operating system settings.
Closes: #8183
This PR changes the compare page to make the "..." in the between branches a clickable
link. This changes the comparison type from "..." to "..". Similarly it makes the
initial compare icon clickable to switch the head and base branches.
Signed-off-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: Lauris BH <lauris@nix.lv>
Co-authored-by: Lunny Xiao <xiaolunwen@gmail.com>
When rendering source in org mode there is a mistake in the highlight code that
causes a panic.
This PR fixes this.
Fix#17139
Signed-off-by: Andrew Thornton <art27@cantab.net>
* DBContext is just a Context
This PR removes some of the specialness from the DBContext and makes it context
This allows us to simplify the GetEngine code to wrap around any context in future
and means that we can change our loadRepo(e Engine) functions to simply take contexts.
Signed-off-by: Andrew Thornton <art27@cantab.net>
* fix unit tests
Signed-off-by: Andrew Thornton <art27@cantab.net>
* another place that needs to set the initial context
Signed-off-by: Andrew Thornton <art27@cantab.net>
* avoid race
Signed-off-by: Andrew Thornton <art27@cantab.net>
* change attachment error
Signed-off-by: Andrew Thornton <art27@cantab.net>
The io/ioutil package has been deprecated as of Go 1.16, see
https://golang.org/doc/go1.16#ioutil. This commit replaces the existing
io/ioutil functions with their new definitions in io and os packages.
Signed-off-by: Eng Zer Jun <engzerjun@gmail.com>
Co-authored-by: techknowlogick <techknowlogick@gitea.io>
* Ignore Sync errors on pipes when doing `CheckAttributeReader.CheckPath`
* apply env patch
* Drop the Sync and fix a number of issues with the Close function
Signed-off-by: Andrew Thornton <art27@cantab.net>
* add logs for DBIndexer and CheckPath
* Fix some more closing bugs
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Add test case for language_stats
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Update modules/indexer/stats/db.go
Co-authored-by: Lauris BH <lauris@nix.lv>
Co-authored-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: Lauris BH <lauris@nix.lv>
Co-authored-by: 6543 <6543@obermui.de>
Some people still appear to report unclosed cat-files. This PR simply adds the caller
to the process descriptor for the CatFileBatch and CatFileBatchCheck calls.
Signed-off-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: techknowlogick <techknowlogick@gitea.io>
This PR extends #16594 to allow LDAP to be able to be set to skip local 2FA too. The technique used here would be extensible to PAM and SMTP sources.
Signed-off-by: Andrew Thornton <art27@cantab.net>
* Clean-up HookPreReceive and restore functionality for pushing non-standard refs
There was an inadvertent breaking change in #15629 meaning that notes refs and other
git extension refs will be automatically rejected.
Further following #14295 and #15629 the pre-recieve hook code is untenably long and
too complex.
This PR refactors the hook code and removes the incorrect forced rejection of
non-standard refs.
Fix#16688
Signed-off-by: Andrew Thornton <art27@cantab.net>
When converting repositories from forks to normal the root NumFork needs to be
decremented too.
Fix#17026
Signed-off-by: Andrew Thornton <art27@cantab.net>
The rollback functionality in
services/repository/repository.go:ForkRepository is incorrect and could
lead to a deadlock as it uses DeleteRepository to delete the rolled-back
repository - a function which creates its own transaction.
This PR adjusts the rollback function to only use RemoveAll as any
database changes will be automatically rolled-back. It also handles
panics and adjusts the Close within WithTx to ensure that if there is a
panic the session will always be closed.
Signed-off-by: Andrew Thornton <art27@cantab.net>
Fixes#16381
Note that changes to unprotected files via the web editor still cannot be pushed directly to the protected branch. I could easily add such support for edits and deletes if needed. But for adding, uploading or renaming unprotected files, it is not trivial.
* Extract & Move GetAffectedFiles to modules/git
When the external context is cancelled it is possible for the
GitLogReader to not itself be Closed.
This PR does three things:
1. Instead of adding a plain defer it wraps the `g.Close` in a func as
`g` may change.
2. It adds the missing explicit g.Close - although the defer fix makes
this unnecessary.
3. It passes down the external context as the base context for the
GitLogReader meaning that the cancellation of the external context will
pass down automatically.
Fix#17007
Signed-off-by: Andrew Thornton <art27@cantab.net>
Replaces #16262
Replaces #16250
Replaces #14833
This PR first implements a `git check-attr` pipe reader - using `git check-attr --stdin -z --cached` - taking account of the change in the output format in git 1.8.5 and creates a helper function to read a tree into a temporary index file for that pipe reader.
It then wires this in to the language stats helper and into the git diff generation.
Files which are marked generated will be folded by default.
Fixes#14786Fixes#12653
