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docs(plan): pin npa:processedUpTo storage and npa:rootNanopub semantics

Progress counter npa:processedUpTo now explicitly lives inside its own
npass:<trustStateHash> graph (drops atomically with DROP GRAPH on
trust-state flip). npa:rootNanopub rule stated: object of
gen:hasRootDefinition, or <thisNP> when the triple is absent (transition
case); updates therefore share the original root's IRI with the root's
own self-referential declaration.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

296 of 554 branches covered (53.43%)

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