Small documentation improvements and fix warnings

[tsmbland]

As mentioned in #352, the documentation build raises lots of warnings. We get even more warnings if we use the nitpick configuration in conf.py (which is a good idea because it enables useful checks like checking internal links)

With the help of copilot, I've gone through most of these warnings and either fixed them up or suppressed them if not important. I've tried to manually check that all the changes are appropriate and don't introduce any more breakages, and I'm fairly confident. In any case, this is surely a step in the right direction.

Aside from fixing mistakes, the only major change is to make a dedicated section for preset consumption files, and add a bit more detail about the typical file structure for models.

Closes #352 apart from a few warnings, mostly to do with the API docs and pandas/xarray which I'm not too fussed about for now

[Copilot]

Pull request overview

This PR fixes documentation warnings that occur when building the Sphinx documentation, as reported in issue #352. The changes enable nitpicky mode in the Sphinx configuration to enable better documentation quality checks, and address the warnings that surfaced as a result.

Key changes include:

• Corrected cross-references and Sphinx directives throughout docstrings and RST files
• Standardized documentation formatting (backticks for inline code, proper directive syntax)
• Created a new dedicated section for preset consumption files with detailed documentation
• Updated intersphinx URLs to use stable docs and HTTPS

Reviewed changes

Copilot reviewed 18 out of 19 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/conftest.py	Removed reference to non-existent muse.decorators module from registry saving fixture
src/muse/utilities.py	Updated docstring formatting: changed "Arguments:" to "Args:" and added proper RST backticks
src/muse/timeslices.py	Added blank lines and backticks to fix docstring formatting
src/muse/readers/csv.py	Reformatted module docstring with proper list formatting and consistent terminology
src/muse/objectives.py	Fixed cross-references to point to correct function names in muse.costs
src/muse/filters.py	Added missing spend_limit to __all__ exports list
src/muse/demand_share.py	Fixed docstring formatting, corrected "it's" to "its", updated directive names and references
src/muse/carbon_budget.py	Simplified return documentation format
docs/installation/pipx-based.rst	Fixed indentation of code-block directive
docs/inputs/toml_primer.rst	Changed code-block language identifiers to lowercase (introduces minor inconsistency)
docs/inputs/toml.rst	Fixed section header lengths, updated cross-references, corrected spelling errors, removed broken link syntax
docs/inputs/preset_commodity_demands.rst	New file documenting preset consumption CSV format
docs/inputs/inputs_csv.rst	Added label and included new preset_commodity_demands in table of contents
docs/inputs/index.rst	Added file structure example and improved introduction
docs/inputs/correlation_files.rst	Added reference label
docs/inputs/commodities_io.rst	Fixed section header underline length
docs/application-flow.rst	Fixed typos (constrains→constraints), updated variable names in diagrams, corrected reference syntax
docs/api.rst	Reorganized API member lists to reflect actual module structure (moved LP functions to separate module)
docs/conf.py	Enabled nitpicky mode, updated intersphinx URLs to stable versions with HTTPS

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