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docs(nav): nest the Getting Started chapters and flatten REFERENCE - #590

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Two navigation fixes, both verified by parsing the rendered sidebar rather than by reading the source.

Getting Started

The four notebooks were listed above the first heading, so they read as a loose list rather than as part of the Quick start they belong to. They are now its sub-chapters, and the ecosystem map — which sat beside Getting Started in the OVERVIEW group — is its closing chapter:

Getting Started
    Quick start
        A minimal CPP analysis
        Quick start with AAanalysis
        Slow start with AAanalysis
        Plotting Prelude
    The two APIs
    Decision Map
    The AAanalysis Ecosystem
        Ecosystem map

A toctree takes its sidebar position from where it sits in the file, and a section heading captures everything after it — so "last and at the top level" is only expressible as a section of its own. Hence the short closing section, which says what the map covers and links to it.

REFERENCE: seven top-level chapters down to five

API                     (↳ Beta Features)
API (Pipelines)
Data                    (↳ Data Tables, Data Schemas)
Glossary
Scientific References

Beta Features moves under API, since it qualifies the API surface rather than standing beside it. Data Tables and Data Schemas move under a new Data chapter that introduces both and says which answers which question: what ships with the package, versus what the frames it returns contain.

Full build: no toctree warnings, nothing orphaned, and the rendered sidebar matches the tree above.

🤖 Generated with Claude Code

Getting Started listed its four notebooks above the first heading, so they
read as a loose list rather than as part of the Quick start they belong
to. They are now the sub-chapters of Quick start, and the ecosystem map,
which used to sit beside Getting Started in the OVERVIEW group, is its
closing chapter:

    Getting Started
        Quick start
            A minimal CPP analysis
            Quick start with AAanalysis
            Slow start with AAanalysis
            Plotting Prelude
        The two APIs
        Decision Map
        The AAanalysis Ecosystem
            Ecosystem map

A toctree takes its sidebar position from where it sits in the file, and a
section heading captures everything after it, so "last and at the top
level" is only expressible as a section of its own. Hence the short
closing section, which says what the map covers and links to it.

REFERENCE had seven top-level chapters, four of which were pages nobody
would look for on their own. It now has five: Beta Features moves under
API, since it qualifies the API surface rather than standing beside it,
and Data Tables and Data Schemas move under a new Data chapter that
introduces both and says which one answers which question - what ships
with the package, versus what the frames it returns contain.

Verified on a full build: no toctree warnings, nothing orphaned, and the
rendered sidebar matches the tree above.

Co-Authored-By: Claude Fable 5.1 <[email protected]>
@codecov

codecov Bot commented Sep 18, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.39%. Comparing base (b0334c6) to head (eb1229e).
⚠️ Report is 9 commits behind head on master.

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@@           Coverage Diff           @@
##           master     #590   +/-   ##
=======================================
  Coverage   95.39%   95.39%           
=======================================
  Files         222      222           
  Lines       23387    23387           
  Branches     4073     4073           
=======================================
  Hits        22309    22309           
  Misses        631      631           
  Partials      447      447           

see 2 files with indirect coverage changes

Components Coverage Δ
cpp_core 95.97% <ø> (ø)
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