docs(docs): second whole-repo pass over the non-API docs and indexes (#1103)

[JarryShaw]

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• Followed the coding style (make pylint, make mypy, make isort)

• make test passes, and a test case covers the change. Narrow runs only, listed below.

• Added a changelog entry under docs/source/changelog/ and regenerated CHANGELOG.md, if the change is user-visible: N/A — centralised in docs(changelog): shared 1.5.0 changelog — long-lived, merges last (#610, #616, #617, #618, #620) #657

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Summary

#1103 second whole-repo pass, docs slice.

• Accuracy: the protocol hierarchy graph puts IPsec under Internet, not IP,
  and draws IPv6_Ext as the base of every IPv6 extension header, AH, ESP and
  HIP included; ext.rst's shipped-protocol table gains its IPv6_Ext row.
• Accuracy: SeekableReader has 14 positional-only methods, not 13 (_fill,
  fix(foundation): extracting from a pipe or non-seekable stream silently stops early (870 of 1,117 frames) #1586); mint-criterion's AppType.missing pointer moves to
  apptype.py:2958; the pcapkit-vendor help transcript reads "options:", as
  argparse prints it on every supported Python.
• Directives: versionchanged 1.5.0 on the CLI section, for -P and -L taking
  effect and -L's closed set of layer names (layer= and protocol= are silently ignored, as are CLI -L and -P #356).
• Conventions: documentation.rst records that a hand-written .. data:: or
  .. function:: takes the bare name under its .. module::, with :module:
  where the object lives elsewhere (docs: 36 ambiguous cross-reference warnings from registry members named dict, set and type #1775).
• Toctrees: dumpkit lists common, its base-class page, first, as every
  sibling index does.

tests/project: 950 passed, 1 skipped.

Refs #1103

[JarryShaw]

Verdict: GOOD TO GO at d6361ffdc. A Sonnet cross-review (author: Opus) found no blocking findings. Scope stays inside the slice, the AST guard is identical against main, and every directive was checked against the release tags. The merged build of all nine second-pass heads has 18 warnings, the same as main. tests/project: 950 passed, 1 skipped, 3 warnings, 3670 subtests passed.