This PR refines some of the changes from the logging refactor to tackle
some issues as well as simplify the code.

Changes:
## `ExecMode` added to `OutputSettings`:
- ExecMode is critical to setting up the logger and controls how logs
are written, so from this perspective I think it makes sense that
ExecMode fits here
- Moving ExecMode here allows the logger to be setup in SnakemakeAPI,
which has multiple positive effects: the logger only needs to be setup
once in all of Snakemake's lifecycle, the logger is setup before the
workflow, allowing for workflow files to use the logger (#3558), and the
logger does not need to manage state anymore.
- This could be seen as a breaking change, though I've set the default
for this field to be ExecMode.DEFAULT so existing callers would be
unaffected.

## Setup logger no longer dependent on
`executor_plugin.common_settings.dryrun_exec`
- Another reason the logger had to be setup late in the Snakemake
lifecycle was that the stdout setting was dependent on this executor
plugin setting
- During refactoring I didn't question this, but now after looking at
most of the executor plugins, I haven't seen any that use this, so I'm
not sure the rationale behind tying stdout to this. @johanneskoester do
you happen to know?

## QueueHandler only used for plugins
- Only spin up queue overhead for logger plugins if they are being used.

## Added more tests
- Added test for specifiyng logger in Snakefile

### QC
<!-- Make sure that you can tick the boxes below. -->

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Added configurable output settings to control log level overrides,
plugin handler usage, and file logging.
* Added comprehensive logging tests and supporting test workflows to
validate logging behavior and failure scenarios.

* **Bug Fixes**
* Centralized and stabilized logger initialization for more consistent
logging across runs.

* **Refactor**
* Simplified logging setup by removing mode-based branching and
consolidating output-settings creation and handler management.

* **Documentation**
  * Documented the logging module and centralized logger management.

* **Chores**
  * Removed an outdated logfile test and updated test coverage.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Johannes Köster <[email protected]>

…(thanks @raffienficiaud) (#3736)

fixes #3719

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Default MILP solver is now chosen automatically from solvers available
in your environment.

* **Improvements**
* Solver selection is more robust by using an ordered list of available
solvers instead of a fixed default.
* Falls back to a sensible bundled solver when others aren’t available.
* Users can still pick a solver explicitly via settings or
configuration.

* **Bug Fixes**
* Reduces failures on systems where the previously assumed default
solver was missing.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

🤖 I have created a release *beep* *boop*
---


##
[9.11.3](v9.11.2...v9.11.3)
(2025-09-16)


### Bug Fixes

* logging refinements
([#3571](#3571))
([47ae16e](47ae16e))
* use proper default and fallback LP solver in scheduler settings
(thanks [@raffienficiaud](https://github.com/raffienficiaud))
([#3736](#3736))
([e00e5aa](e00e5aa))


### Documentation

* mention nodefaults for installation
([a6db049](a6db049))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
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