[docs] nopy: record the seven findings this branch closed

The documentation half of the same work: `DOCS-AUDIT.md` marks §1.3, §1.5,
§2.3, §4.2 (all three points), §5.1, §6.1, §6.2 and §6.5 closed, each keeping
its original text as the record with what closed it quoted underneath, and the
"suggested order of attack" is rewritten to what is actually left — §5.2, §5.3,
the two missing cube READMEs, and the two findings (§2.7, §4.4) that are stated
accurately in `docs/API.md` while the code still behaves as they describe.

`docs/API.md` drops the two entries from its *Known gaps* list that are no
longer gaps, documents the argv and the absent shell, describes the resolution
stack and the error it raises, and inverts the `.default()`/`.describe()`
warning: the order used to matter and no longer does, which is worth saying
outright since the old advice is in the reader's memory and in 15 manifests.

The README's "topological sorting" becomes "in dependency order, with cycle
detection" — the sort never existed, but until this branch neither did the
thing a sort would have been for — and `--no-history` is spelled
`--no-save-history` wherever it appears.

One line of code rides along, because it is what a `docs/API.md` note has been
asking for: `CubePackageRef` is re-exported from `src/index.ts`, so importing
`NopyConfig` from `@bitsquare/nopy` no longer gives you a type whose own
members you cannot name. The note in `docs/API.md` saying it is missing goes
with it.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DCzYTAm9QUhvLNr2EpdagJ

packages/nopy/src/index.ts

@@ -10,6 +10,7 @@ export type { Assignment, Origin, TVariables, Value } from './nopy.common.js';
 // Variables
 export { MASK, Variable, Variables } from './nopy.common.js';
 export type {
+  CubePackageRef,
   ExecutionConfig,
   HistoryConfig,
   LogConfig,