refactor(build): finalize Doxygen input paths and install rules

[kcenon]

What

Summary

Final sub-issue of EPIC #531. Repoint Doxygen INPUT/INCLUDE_PATH and cmake/documentation.cmake DOXYGEN_INPUT to the canonical post-migration layout, and tighten cmake/install.cmake to reflect the actual install rules now in effect.

Change Type

• Feature
• Bugfix
• Refactor (no functional changes)
• Documentation
• Test
• Chore

Affected Components

• Doxyfile -- INPUT, INCLUDE_PATH
• cmake/documentation.cmake -- DOXYGEN_INPUT
• cmake/install.cmake -- documentation block, deprecation marker
• CHANGELOG.md, docs/CHANGELOG.md -- release notes

Why

Problem Solved

After the four prior sub-issues (#532 -- #535) consolidated headers under include/kcenon/container/, moved .cpp files into src/<subdir>/, deprecated the legacy include/container/ forwarders, and decomposed the top-level CMakeLists.txt into 11 cmake/ modules, three artifacts still carried drift-fix-only state from issue #533 / #535:

1. Doxyfile INCLUDE_PATH still referenced removed roots (core/, values/, internal/, integration/).
2. cmake/documentation.cmake DOXYGEN_INPUT listed ${CMAKE_CURRENT_SOURCE_DIR} as a catch-all (pulling in build artifacts and unrelated metadata) and pointed at a non-existent root mainpage.dox.
3. cmake/install.cmake documentation block still enumerated removed root-level forwarding directories, and the deprecated include/container/ install rule had no recorded removal milestone.

Related Issues

• Closes [#531-5/5] Update Doxygen input paths and install rules #536
• Part of [EPIC] container_system: consolidate scattered headers and standardize layout #531 (final sub-issue)

Who

Reviewers

• @kcenon

When

Urgency

• Normal -- follow standard review process

Target Release

The cleanup itself is part of [Unreleased]. The TODO marker on the deprecated include/container/ install rule names v1.2.0 as the removal milestone, matching the deprecation cycle started in #534/PR #539.

Where

Files Changed

File	Change
Doxyfile	Repoint INCLUDE_PATH; drop temporary layout-disclaimer comment above INPUT
cmake/documentation.cmake	Repoint DOXYGEN_INPUT; align comment with the standalone Doxyfile
cmake/install.cmake	Tidy documentation block; add v1.2.0 TODO marker; drop dropped-rule breadcrumb
CHANGELOG.md	Record under Unreleased > Changed
docs/CHANGELOG.md	Mirror under Unreleased > Changed

API/Database Changes

None. Public C++ API unchanged. CMake export set, package config, target name, namespace, and install destinations are unchanged. The set of installed headers is identical to the pre-refactor state (canonical include/kcenon/container/ + deprecated include/container/).

How

Implementation Highlights

Doxyfile

INPUT was already canonical (set in #538). Only the temporary disclaimer comment was rewritten to describe current state instead of pointing at #533/#536.

INCLUDE_PATH previously listed core values internal integration -- those root directories were removed in #533/PR #538. Replaced with include, include/kcenon/container, and src so Doxygen's preprocessor can resolve #include directives in the new layout.

cmake/documentation.cmake

DOXYGEN_INPUT previously had two issues:

• ${CMAKE_CURRENT_SOURCE_DIR} (source root catch-all) -- pulls in .git/, cmake/, top-level scripts, and the like; doxygen has to filter them via EXCLUDE patterns rather than not loading them in the first place.
• ${CMAKE_CURRENT_SOURCE_DIR}/mainpage.dox -- the file lives at docs/mainpage.dox, not at the source root. The path resolved to a non-existent file and would have produced a Doxygen warning had the target been exercised.

Repointed to the same set of inputs as the standalone Doxyfile: include/kcenon/container/, src/, examples/, utilities/, README.md, and the explicit docs/*.dox pages.

cmake/install.cmake

The install rules themselves are unchanged. Only the comments were rewritten:

• The opening "behaviour mirrors the legacy top-level CMakeLists.txt exactly" disclaimer (true for [#531-4/5] Decompose CMakeLists.txt into cmake/ modules #535 but no longer relevant) was dropped.
• The "directories installed" comment block listed legacy roots (core/, internal/, integration/, messaging/) that haven't been installed since [#531-2/5] Source migration to src/{core,internal,integration,messaging}/ #533. Tightened to the two directories actually being installed.
• The Forwarding headers under include/container/ comment now records the deprecation cycle ([#531-3/5] Mark legacy include/container/ forwarding [[deprecated]] #534, PR refactor(container): deprecate legacy include/container/ forwarding headers #539) and the v1.2.0 removal milestone via a TODO(v1.2.0) marker.
• The breadcrumb explaining the dropped root-level core/internal/integration/messaging install rule was removed -- two PRs have shipped since the rule was removed and the file's git history carries the same information.

Verification

• All 10 Doxyfile INPUT paths and all 4 INCLUDE_PATH entries exist on disk (verified with [ -e <path> ]).
• All 13 ${CMAKE_CURRENT_SOURCE_DIR}/... paths in DOXYGEN_INPUT exist on disk (build/, build_test/, vcpkg/, vcpkg_installed/ are EXCLUDE entries and are expected to be absent until configure/build).
• All install-time paths in cmake/install.cmake exist (container.h, include/kcenon, include/container, cmake/container_system-config.cmake.in).

Local cmake/g++/doxygen toolchains are unavailable in this sandbox; relying on CI for the cmake configure pass, the multi-platform build, ctest, and the Documentation Audit step (per ci-resilience.md).

Testing Done

• Path-existence sanity check for every INPUT and INCLUDE_PATH entry
• Path-existence sanity check for every DOXYGEN_INPUT and install(...) source entry
• Local Doxygen run -- skipped (doxygen not installed in sandbox; CI covers this)
• Local CMake configure + build + ctest -- skipped (cmake not installed in sandbox; CI covers this)
• Local cmake --install build/ --prefix /tmp/inst -- skipped (same reason; install rules unchanged in substance)

Breaking Changes

None.

Rollback Plan

Plain revert of this PR. The five EPIC #531 sub-issue PRs land in order #537 -> #538 -> #539 -> #540 -> this one, so reverting in reverse order is safe.

Checklist

• Code follows project style guidelines
• Self-review completed
• Path-existence verification performed (no cmake/doxygen available locally)
• CHANGELOG.md and docs/CHANGELOG.md updated
• No sensitive data exposed
• Commit follows Conventional Commits
• Issue linked with closing keyword (Closes #536) and EPIC reference (Part of #531)