[#282]:svarga:docs, move docs/ tree under doxy/ — single Doxygen project root, doxy/docs/ holds all sources + build output

Consolidates everything Doxygen-related under doxy/. The top-level
docs/ directory is gone; its contents move as a single subtree to
doxy/docs/ so the Doxygen project (config + theme + sources + build
output) lives in one place.

Moved (git-rename detected, content unchanged — 44 files):
  docs/index.md           → doxy/docs/index.md          (Doxygen mainpage)
  docs/aliases.md         → doxy/docs/aliases.md        (Doxygen INPUT alias page)
  docs/curated/   (18)    → doxy/docs/curated/          (I/O + TOPICS axes)
  docs/reports/   (19)    → doxy/docs/reports/          (project reports tree)
  docs/links/     (4)     → doxy/docs/links/            (Doxyfile @INCLUDE_PATH)
  docs/tags/      (1)     → doxy/docs/tags/             (cppreference TAGFILE)

Build output (untracked, .gitignored — not in the rename set):
  docs/doxygen/   (490+ generated files)   → doxy/docs/doxygen/

Path updates (4 modifications):

  doxy/Doxyfile — all `../docs/X` references rewritten to `docs/X`
  (Doxyfile sits in doxy/ and docs/ is now its sibling):
    OUTPUT_DIRECTORY, WARN_LOGFILE, INPUT, EXCLUDE, USE_MDFILE_AS_MAINPAGE,
    TAGFILES, @INCLUDE_PATH

  scripts/docs-build.sh — post-process target + final message updated
  to doxy/docs/doxygen/html

  .github/workflows/docs.yml — three path references:
    log=docs/doxygen/warnings.log     → doxy/docs/doxygen/warnings.log
    path: docs/doxygen/warnings.log   → doxy/docs/doxygen/warnings.log
    publish_dir: ./docs/doxygen/html  → ./doxy/docs/doxygen/html

  .gitignore — updated for new build path; dropped two mkdocs-era stale
  lines:
    docs/docs/site                    → removed
    site/                             → removed
    docs/doxygen/                     → doxy/docs/doxygen/

Side benefit: the `../../../examples/X` cross-references in some
reports (h5cpp-handle-inventory.md, h5cpp-filters-inventory-and-use-guide.md)
were broken after the earlier reports-tree flattening — they assumed
3-level depth. Reports now live 3 levels deep again (doxy/docs/reports/X.md),
so the existing paths resolve correctly without further editing.

Local rebuild via scripts/docs-build.sh is clean (0 warnings); every
key landing page resolves at doxy/docs/doxygen/html/. The development
server is restarted against the new path.

Author: steven-varga

.github/workflows/docs.yml

@@ -10,7 +10,7 @@ permissions:
 jobs:
   # Doxygen — full project documentation site (API reference + curated
   # I/O+TOPICS axes + COOKBOOK + REPORTS, all generated from headers,
-  # examples, and the docs/{index,aliases,curated,reports}/ markdown).
+  # examples, and the doxy/docs/{index,aliases,curated,reports}/ markdown).
   # Publishes to the gh-pages root; MkDocs has been retired.
   deploy-doxygen:
     runs-on: ubuntu-latest
@@ -39,7 +39,7 @@ jobs:
       - name: Summarise Doxygen warnings
         if: always()
         run: |
-          log=docs/doxygen/warnings.log
+          log=doxy/docs/doxygen/warnings.log
           if [[ -f $log ]]; then
             count=$(wc -l < $log)
             echo "::notice::Doxygen warnings: $count lines (see uploaded artifact 'doxygen-warnings')"
@@ -53,13 +53,13 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: doxygen-warnings
-          path: docs/doxygen/warnings.log
+          path: doxy/docs/doxygen/warnings.log
           if-no-files-found: ignore
           retention-days: 30
 
       - name: Deploy Doxygen to gh-pages root
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/doxygen/html
+          publish_dir: ./doxy/docs/doxygen/html
           keep_files: true

.gitignore

@@ -158,6 +158,4 @@ data/
 # =============================================================================
 # Documentation build output
 # =============================================================================
-docs/docs/site
-site/
-docs/doxygen/
+doxy/docs/doxygen/

doxy/Doxyfile

@@ -1,6 +1,6 @@
 # Doxyfile 1.9.x — H5CPP API reference
 # Run from the doxy/ directory: doxygen Doxyfile
-# Output lands in ../docs/doxygen/html/ (separate from MkDocs site/)
+# Output lands in docs/doxygen/html/ (separate from MkDocs site/)
 
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = H5CPP
@@ -12,7 +12,7 @@ PROJECT_NAME           = H5CPP
 PROJECT_NUMBER         = $(H5CPP_DOXYGEN_VERSION)
 PROJECT_BRIEF          = "Modern C++ templates for HDF5 serial and parallel I/O"
 PROJECT_LOGO           =
-OUTPUT_DIRECTORY       = ../docs/doxygen
+OUTPUT_DIRECTORY       = docs/doxygen
 CREATE_SUBDIRS         = NO
 ALLOW_UNICODE_NAMES    = NO
 OUTPUT_LANGUAGE        = English
@@ -47,25 +47,25 @@ WARN_NO_PARAMDOC       = NO
 # Emit warnings into a logfile alongside stderr so CI can upload it as an
 # artifact for coverage-tracking visibility. The file lives in the build dir
 # so it's picked up by the workflow's actions/upload-artifact step.
-WARN_LOGFILE           = ../docs/doxygen/warnings.log
+WARN_LOGFILE           = docs/doxygen/warnings.log
 
 # Input: API headers + README as main page + local Doxygen pages +
 # the curated reports tree + the alias-vocabulary reference. Conceptual
 # guides with Material icons/images still live in MkDocs; Doxygen
 # carries the API reference and the design/inventory prose that
 # accompanies it.
 INPUT                  = ../h5cpp \
-                         ../docs/index.md \
-                         ../docs/reports \
-                         ../docs/curated \
-                         ../docs/aliases.md \
+                         docs/index.md \
+                         docs/reports \
+                         docs/curated \
+                         docs/aliases.md \
                          ../examples \
                          .
 
 FILE_PATTERNS          = *.cpp *.hpp *.h *.md *.dox
 RECURSIVE              = YES
 
-EXCLUDE                = ../docs/doxygen
+EXCLUDE                = docs/doxygen
 # ../examples/ is added to INPUT only so README.md files become Doxygen
 # pages. Exclude the example *source* files from INPUT scanning — they're
 # already handled as `\example` listings via EXAMPLE_PATH below and shouldn't
@@ -130,7 +130,7 @@ EXAMPLE_PATH           = ../examples/attributes \
 EXAMPLE_PATTERNS       = *.cpp *.hpp *.h
 EXAMPLE_RECURSIVE      = YES
 
-USE_MDFILE_AS_MAINPAGE = ../docs/index.md
+USE_MDFILE_AS_MAINPAGE = docs/index.md
 
 # Index and layout
 ALPHABETICAL_INDEX     = NO
@@ -159,10 +159,10 @@ ENUM_VALUES_PER_LINE   = 4
 GENERATE_LATEX         = NO
 
 # Tag files for cross-links
-TAGFILES              += "../docs/tags/cppreference-doxygen-web.tag.xml=https://en.cppreference.com/"
+TAGFILES              += "docs/tags/cppreference-doxygen-web.tag.xml=https://en.cppreference.com/"
 
 # Alias includes — each file adds ALIASES lines
-@INCLUDE_PATH          = ../docs/links
+@INCLUDE_PATH          = docs/links
 @INCLUDE               = h5cpp.txt
 @INCLUDE               = hdf5.txt
 @INCLUDE               = linalg.txt