Use precise PSR-4 autoload prefixes and flatten src/<Namespace>/ across packages

Follow-up from #1078.

Several packages declare a PSR-4 autoload prefix broader than the namespace their classes actually live under, e.g. guides-markdown declares "phpDocumentor\\Guides\\": "src/" even though every class is under phpDocumentor\Guides\Markdown\.... This forces a non-optimized autoloader (common in dev environments) to check that package's src/ for classes anywhere under phpDocumentor\Guides\, not just its own subset. Packages with the same imprecise prefix: guides-code, guides-graphs, guides-markdown, guides-pages, guides-restructured-text, guides-theme-bootstrap, guides-theme-rst.

Fix, per the direction agreed in #1078:

• Flatten src// into src/ for the affected packages (guides-cli already uses this flat layout, so there's precedent in the monorepo).
• Declare a precise PSR-4 prefix per package, e.g. "phpDocumentor\\Guides\\Markdown\\": "src/".
• Do the moves in a dedicated commit with no other changes, so git recognizes them as renames rather than delete+add.

guides-restructured-text needs special handling: it has classes under both RestructuredText/ and a separate top-level PHPStan/ subtree, so it isn't a clean single-namespace-per-package fit like the others.

Compare the Composer PSR-4 declarations and src layouts in guides-code, guides-graphs, guides-markdown, guides-pages, guides-restructured-text, guides-theme-bootstrap, and guides-theme-rst with the flat layout in guides-cli and the direction from #1078. Flatten the affected namespaces, use precise package prefixes, and keep moves in a dedicated rename-only commit. Account separately for the PHPStan subtree in guides-restructured-text.