docs: modernize documentation structure

[galjos]

Scope

• reorganize the manual around getting started, analyses, data, CLI reference, Python functions and development
• add focused RDF, MSD, VACF, vibration and momentum guides
• document package architecture, analysis extensions, validation and releases
• adopt the shared Furo layout and logo treatment used by the other MolarVerse projects
• replace the legacy Pages job with strict pull-request builds and GitHub Pages deployment actions

Re-evaluation after #168 and #169

• merged the current dev branch into this branch
• documented float64 trajectory parsing, fixed-bit compatibility paths, bounded fallbacks and parallel-work limits
• corrected the RDF, MSD and momentum method descriptions to match the merged implementations
• corrected the pull-request merge guidance and scientific units
• fixed the mobile back-to-top control so it cannot cover equations or figures

Validation

• 867 passed, 4 skipped in release type-checking mode
• strict Sphinx HTML build with warnings as errors
• strict Sphinx link check with warnings as errors
• rendered checks at 320x568, 375x812, 768x1024, 844x390 and 1440x900
• no page-level overflow, broken images or browser console errors on the landing, VACF, momentum, validation, output-schema and function-index pages
• mobile navigation, logo alignment, scientific tables, VACF equation and VACF figure inspected directly

This PR remains a draft and is not merged. The repository Pages source is still
gh-pages; changing that setting is outside this draft.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.79%. Comparing base (c37008e) to head (ec49ddc).

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #167   +/-   ##
=======================================
  Coverage   93.79%   93.79%           
=======================================
  Files         176      176           
  Lines        9094     9094           
=======================================
  Hits         8530     8530           
  Misses        564      564           

Flag	Coverage Δ
unittests	93.79% <ø> (ø)

Files with missing lines	Coverage Δ
PQAnalysis/io/restart_file/api.py	100.00% <ø> (ø)

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[github-actions]

PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type	number	%	previous	difference
code	15321	45.57	NC	NC
docstring	12809	38.10	NC	NC
comment	474	1.41	NC	NC
empty	5015	14.92	NC	NC

Duplication

	now	previous	difference
nb duplicated lines	0	NC	NC
percent duplicated lines	0.000	NC	NC

Messages by category

type	number	previous	difference
convention	15	NC	NC
refactor	134	NC	NC
warning	19	NC	NC
error	5	NC	NC

% errors / warnings by module

module	error	warning	refactor	convention
PQAnalysis.type_checking	40.00	0.00	0.00	0.00
PQAnalysis.atomic_system.atomic_system	20.00	10.53	6.72	0.00
PQAnalysis.analysis.vibrational.vibrational_analysis	20.00	0.00	7.46	0.00
PQAnalysis	20.00	0.00	0.00	0.00
PQAnalysis.analysis.vacf._vacf_kernel_py	0.00	10.53	1.49	0.00
PQAnalysis.topology.init	0.00	10.53	0.00	0.00
PQAnalysis.tools.traj_to_com_traj	0.00	10.53	0.00	0.00
PQAnalysis.io.traj_file._process_lines_py	0.00	10.53	0.00	0.00
PQAnalysis.io.moldescriptor_reader	0.00	10.53	0.00	0.00
PQAnalysis.tools.add_molecule	0.00	5.26	4.48	0.00
PQAnalysis.analysis.rdf._rdf_kernel_py	0.00	5.26	2.24	0.00
PQAnalysis.analysis.msd._msd_kernel_py	0.00	5.26	2.24	0.00
PQAnalysis.io.conversion_api	0.00	5.26	1.49	0.00
PQAnalysis.version	0.00	5.26	0.00	0.00
PQAnalysis.utils.custom_logging	0.00	5.26	0.00	0.00
PQAnalysis.io.write_api	0.00	5.26	0.00	0.00
PQAnalysis.core.atom.element	0.00	0.00	13.43	13.33
PQAnalysis.analysis.msd.msd	0.00	0.00	6.72	33.33
PQAnalysis.analysis.rdf.rdf	0.00	0.00	6.72	6.67
PQAnalysis.io.nep.nep_writer	0.00	0.00	5.22	6.67
PQAnalysis.analysis.vacf.vacf	0.00	0.00	4.48	13.33
PQAnalysis.io.traj_file._slab_parser_py	0.00	0.00	3.73	0.00
PQAnalysis.analysis.vacf.spectrum	0.00	0.00	3.73	0.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	2.99	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	2.24	0.00
PQAnalysis.core.residue	0.00	0.00	2.24	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	1.49	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	1.49	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	1.49	0.00
PQAnalysis.io.traj_file.raw_frame_reader	0.00	0.00	1.49	0.00
PQAnalysis.core.cell.cell	0.00	0.00	1.49	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	1.49	0.00
PQAnalysis.analysis.vacf.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.spectrum_broadening.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.momentum.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.vibrational.vibrational_input_file_reader	0.00	0.00	0.75	6.67
PQAnalysis.traj.formats	0.00	0.00	0.75	0.00
PQAnalysis.topology.topology	0.00	0.00	0.75	0.00
PQAnalysis.topology.selection	0.00	0.00	0.75	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	0.75	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.formats	0.00	0.00	0.75	0.00
PQAnalysis.analysis.momentum.momentum	0.00	0.00	0.75	0.00
PQAnalysis.analysis.vacf.vacf_input_file_reader	0.00	0.00	0.00	6.67
PQAnalysis.analysis.rdf.rdf_input_file_reader	0.00	0.00	0.00	6.67
PQAnalysis.analysis.msd.msd_input_file_reader	0.00	0.00	0.00	6.67

Messages

message id	occurrences
too-many-positional-arguments	29
too-many-arguments	29
duplicate-code	18
too-many-locals	16
too-many-instance-attributes	13
invalid-name	12
too-complex	9
fixme	9
inconsistent-return-statements	8
too-many-branches	5
missing-type-doc	4
too-many-return-statements	3
too-many-lines	3
unused-import	2
too-many-statements	2
redefined-builtin	2
missing-kwoa	2
use-set-for-membership	1
unexpected-keyword-arg	1
too-many-public-methods	1
possibly-used-before-assignment	1
no-member	1
missing-param-doc	1
arguments-differ	1