This was originally removed in #18886
but it looks like it snuck back in #18828
during a bad merge

This was originally removed in
#18886 but it looks like it
snuck back in #18828 during a
[bad
merge](4cd3d91).

Noticed while looking at Synapse setup and startup (just by happen
stance).

I don't think this has adverse effects on Synapse actually working and
`start_background_tasks()` can be called multiple times.


### Is there a good way to audit all of these merges?

As I would like to see the conflicts for each merge.

This works but it's still hard to notice anything is wrong:

```
git log --remerge-diff <commit-sha>
```

> shows the difference from mechanical merge result and the result that
is actually recorded in a merge commit

via
https://stackoverflow.com/questions/15277708/how-do-you-see-show-a-git-merge-conflict-resolution-that-was-done-given-a-mer/71181334#71181334

The following better. Specify the version range to the commit right
before the merge to the merge. And can even specify which file to look
at to make it more obvious with the hindsight we have now.

```
git log --remerge-diff <merge-commit-sha>~1..<merge-commit-sha> -- synapse/server.py
```

Example:
```
git log --remerge-diff 4cd3d91~1..4cd3d91 -- synapse/server.py
```

Deployments that make use of the
[synapse-s3-storage-provider](https://github.com/matrix-org/synapse-s3-storage-provider)
module must upgrade to
[v1.6.0](https://github.com/matrix-org/synapse-s3-storage-provider/releases/tag/v1.6.0).
Using older versions of the module with this release of Synapse will prevent
users from being able to upload or download media.

No significant changes since 1.140.0rc1.

- Add [a new Media Query by ID Admin API](https://element-hq.github.io/synapse/v1.140/admin_api/media_admin_api.html#query-a-piece-of-media-by-id) that allows server admins to query and investigate the metadata of local or cached remote media via
  the `origin/media_id` identifier found in a [Matrix Content URI](https://spec.matrix.org/v1.14/client-server-api/#matrix-content-mxc-uris). ([\element-hq#18911](element-hq#18911))
- Add [a new Fetch Event Admin API](https://element-hq.github.io/synapse/v1.140/admin_api/fetch_event.html) to fetch an event by ID. ([\element-hq#18963](element-hq#18963))
- Update [MSC4284: Policy Servers](matrix-org/matrix-spec-proposals#4284) implementation to support signatures when available. ([\element-hq#18934](element-hq#18934))
- Add experimental implementation of the `GET /_matrix/client/v1/rtc/transports` endpoint for the latest draft of [MSC4143: MatrixRTC](matrix-org/matrix-spec-proposals#4143). ([\element-hq#18967](element-hq#18967))
- Expose a `defer_to_threadpool` function in the Synapse Module API that allows modules to run a function on a separate thread in a custom threadpool. ([\element-hq#19032](element-hq#19032))

- Fix room upgrade `room_config` argument and documentation for `user_may_create_room` spam-checker callback. ([\element-hq#18721](element-hq#18721))
- Compute a user's last seen timestamp from their devices' last seen timestamps instead of IPs, because the latter are automatically cleared according to `user_ips_max_age`. ([\element-hq#18948](element-hq#18948))
- Fix bug where ephemeral events were not filtered by room ID. Contributed by @frastefanini. ([\element-hq#19002](element-hq#19002))
- Update Synapse main process version string to include git info. ([\element-hq#19011](element-hq#19011))

- Explain how `Deferred` callbacks interact with logcontexts. ([\element-hq#18914](element-hq#18914))
- Fix documentation for `rc_room_creation` and `rc_reports` to clarify that a `per_user` rate limit is not supported. ([\element-hq#18998](element-hq#18998))

- Remove deprecated `LoggingContext.set_current_context`/`LoggingContext.current_context` methods which already have equivalent bare methods in `synapse.logging.context`. ([\element-hq#18989](element-hq#18989))
- Drop support for unstable field names from the long-accepted [MSC2732](matrix-org/matrix-spec-proposals#2732) (Olm fallback keys) proposal. ([\element-hq#18996](element-hq#18996))

- Cleanly shutdown `SynapseHomeServer` object, allowing artifacts of embedded small hosts to be properly garbage collected. ([\element-hq#18828](element-hq#18828))
- Update OEmbed providers to use 'X' instead of 'Twitter' in URL previews, following a rebrand. Contributed by @HammyHavoc. ([\element-hq#18767](element-hq#18767))
- Fix `server_name` in logging context for multiple Synapse instances in one process. ([\element-hq#18868](element-hq#18868))
- Wrap the Rust HTTP client with `make_deferred_yieldable` so it follows Synapse logcontext rules. ([\element-hq#18903](element-hq#18903))
- Fix the GitHub Actions workflow that moves issues labeled "X-Needs-Info" to the "Needs info" column on the team's internal triage board. ([\element-hq#18913](element-hq#18913))
- Disconnect background process work from request trace. ([\element-hq#18932](element-hq#18932))
- Reduce overall number of calls to `_get_e2e_cross_signing_signatures_for_devices` by increasing the batch size of devices the query is called with, reducing DB load. ([\element-hq#18939](element-hq#18939))
- Update error code used when an appservice tries to masquerade as an unknown device using [MSC4326](matrix-org/matrix-spec-proposals#4326). Contributed by @tulir @ Beeper. ([\element-hq#18947](element-hq#18947))
- Fix `no active span when trying to log` tracing error on startup (when OpenTracing is enabled). ([\element-hq#18959](element-hq#18959))
- Fix `run_coroutine_in_background(...)` incorrectly handling logcontext. ([\element-hq#18964](element-hq#18964))
- Add debug logs wherever we change current logcontext. ([\element-hq#18966](element-hq#18966))
- Update dockerfile metadata to fix broken link; point to documentation website. ([\element-hq#18971](element-hq#18971))
- Note that the code is additionally licensed under the [Element Commercial license](https://github.com/element-hq/synapse/blob/develop/LICENSE-COMMERCIAL) in SPDX expression field configs. ([\element-hq#18973](element-hq#18973))
- Fix logcontext handling in `timeout_deferred` tests. ([\element-hq#18974](element-hq#18974))
- Remove internal `ReplicationUploadKeysForUserRestServlet` as a follow-up to the work in element-hq#18581 that moved device changes off the main process. ([\element-hq#18988](element-hq#18988))
- Switch task scheduler from raw logcontext manipulation to using the dedicated logcontext utils. ([\element-hq#18990](element-hq#18990))
- Remove `MockClock()` in tests. ([\element-hq#18992](element-hq#18992))
- Switch back to our own custom `LogContextScopeManager` instead of OpenTracing's `ContextVarsScopeManager` which was causing problems when using the experimental `SYNAPSE_ASYNC_IO_REACTOR` option with tracing enabled. ([\element-hq#19007](element-hq#19007))
- Remove `version_string` argument from `HomeServer` since it's always the same. ([\element-hq#19012](element-hq#19012))
- Remove duplicate call to `hs.start_background_tasks()` introduced from a bad merge. ([\element-hq#19013](element-hq#19013))
- Split homeserver creation (`create_homeserver`) and setup (`setup`). ([\element-hq#19015](element-hq#19015))
- Swap near-end-of-life `macos-13` GitHub Actions runner for the `macos-15-intel` variant. ([\element-hq#19025](element-hq#19025))
- Introduce `RootConfig.validate_config()` which can be subclassed in `HomeServerConfig` to do cross-config class validation. ([\element-hq#19027](element-hq#19027))
- Allow any command of the `release.py` script to accept a `--gh-token` argument. ([\element-hq#19035](element-hq#19035))

* Bump Swatinem/rust-cache from 2.8.0 to 2.8.1. ([\element-hq#18949](element-hq#18949))
* Bump actions/cache from 4.2.4 to 4.3.0. ([\element-hq#18983](element-hq#18983))
* Bump anyhow from 1.0.99 to 1.0.100. ([\element-hq#18950](element-hq#18950))
* Bump authlib from 1.6.3 to 1.6.4. ([\element-hq#18957](element-hq#18957))
* Bump authlib from 1.6.4 to 1.6.5. ([\element-hq#19019](element-hq#19019))
* Bump bcrypt from 4.3.0 to 5.0.0. ([\element-hq#18984](element-hq#18984))
* Bump docker/login-action from 3.5.0 to 3.6.0. ([\element-hq#18978](element-hq#18978))
* Bump lxml from 6.0.0 to 6.0.2. ([\element-hq#18979](element-hq#18979))
* Bump phonenumbers from 9.0.13 to 9.0.14. ([\element-hq#18954](element-hq#18954))
* Bump phonenumbers from 9.0.14 to 9.0.15. ([\element-hq#18991](element-hq#18991))
* Bump prometheus-client from 0.22.1 to 0.23.1. ([\element-hq#19016](element-hq#19016))
* Bump pydantic from 2.11.9 to 2.11.10. ([\element-hq#19017](element-hq#19017))
* Bump pygithub from 2.7.0 to 2.8.1. ([\element-hq#18952](element-hq#18952))
* Bump regex from 1.11.2 to 1.11.3. ([\element-hq#18981](element-hq#18981))
* Bump serde from 1.0.224 to 1.0.226. ([\element-hq#18953](element-hq#18953))
* Bump serde from 1.0.226 to 1.0.228. ([\element-hq#18982](element-hq#18982))
* Bump setuptools-rust from 1.11.1 to 1.12.0. ([\element-hq#18980](element-hq#18980))
* Bump twine from 6.1.0 to 6.2.0. ([\element-hq#18985](element-hq#18985))
* Bump types-pyyaml from 6.0.12.20250809 to 6.0.12.20250915. ([\element-hq#19018](element-hq#19018))
* Bump types-requests from 2.32.4.20250809 to 2.32.4.20250913. ([\element-hq#18951](element-hq#18951))
* Bump typing-extensions from 4.14.1 to 4.15.0. ([\element-hq#18956](element-hq#18956))

Fix lost logcontext when using `timeout_deferred(...)` and things
actually timeout.

Fix #19087 (our HTTP client
times out requests using `timeout_deferred(...)`
Fix #19066 (`/sync` uses
`notifier.wait_for_events()` which uses `timeout_deferred(...)` under
the hood)


### When/why did these lost logcontext warnings start happening?

```
synapse.logging.context - 107 - WARNING - sentinel - Expected logging context call_later but found POST-2453

synapse.logging.context - 107 - WARNING - sentinel - Expected logging context call_later was lost
```

In #18828, we switched
`timeout_deferred(...)` from using `reactor.callLater(...)` to
[`clock.call_later(...)`](https://github.com/element-hq/synapse/blob/3b59ac3b69f6a2f73a504699b30313d8dcfe4709/synapse/util/clock.py#L224-L313)
under the hood. This meant it started dealing with logcontexts but our
`time_it_out()` callback didn't follow our [Synapse logcontext
rules](https://github.com/element-hq/synapse/blob/3b59ac3b69f6a2f73a504699b30313d8dcfe4709/docs/log_contexts.md).