[codex] Make Protocol tab App Layer ready

[ihsraham]

Summary

Makes the current Nitrolite 1.x Protocol tab App Layer-only and source-bound after the nitrolite / clearnet split from base branch commit f7b0b80 (feat: nitrolite-clearnet separation).

This PR adds a language-agnostic Nitrolite App Layer protocol section derived only from /Users/maharshimishra/Documents/nitrolite/docs/protocol, removes stale current Nitrolite Protocol pages from the visible 1.x Protocol tree, and keeps old VirtualApp/NitroRPC material available under the existing 0.5.x versioned docs.

Current Protocol navigation

• Current 1.x Nitrolite Protocol opens at /nitrolite/protocol/introduction.
• The visible current Protocol sidebar contains only App Layer and its nine source-bound pages.
• The sidebar label is App Layer, not Nitrolite v1 App Layer, because the docs version selector already says 1.x.
• Old current Protocol Reference, Architecture, and old top-level Terminology are not shown in the current Nitrolite Protocol sidebar.
• Clearnet/YNP pages from the base branch remain under /clearnet/** and are not shown in the current Nitrolite Protocol sidebar.
• Version switching from any current Nitrolite Protocol page without a matching 0.5.x doc id falls back to /nitrolite/0.5.x/protocol/introduction, preserving access to the old 0.5 Protocol tree.
• Version switching from 0.5.x Protocol pages without a matching current doc id falls back to /nitrolite/protocol/introduction.

Source coverage matrix

Current page	Source file / sections
docs/nitrolite/protocol/introduction.mdx	docs/protocol/overview.md: design goals, roles, architecture layers, core concepts, protocol version scope
docs/nitrolite/protocol/terminology.mdx	docs/protocol/terminology.md: naming conventions, entities, state, cryptographic, ledger, signing, operation, extension terms
docs/nitrolite/protocol/cryptography-and-signing.mdx	docs/protocol/cryptography.md: algorithms, canonical encoding, digest construction, signature envelope, validation modes, session keys, replay protection
docs/nitrolite/protocol/state-and-ledger-model.mdx	docs/protocol/state-model.md: common fields, channel state, ledger invariant, empty non-home ledger, off-chain/enforcement representations, intent mapping
docs/nitrolite/protocol/channel-lifecycle.mdx	docs/protocol/channel-protocol.md: definition, identifier, lifecycle actions, signing categories, advancement rules, transition families, checkpoint-relevant transitions
docs/nitrolite/protocol/enforcement-and-settlement.mdx	docs/protocol/enforcement.md: enforceability, locked funds, creation, submission, challenge, close, validation, escrow/migration enforcement, failures
docs/nitrolite/protocol/cross-chain-and-assets.mdx	docs/protocol/cross-chain-and-assets.md: unified asset model, normalization, home/non-home ledgers, escrow, cross-chain deposit/withdrawal, migration, replay protection, current notes
docs/nitrolite/protocol/interaction-model.mdx	docs/protocol/interactions.md: transport assumptions, envelope, message types, operations, events, correlation, errors, ordering
docs/nitrolite/protocol/security-and-limitations.mdx	docs/protocol/security-and-limitations.md: maturity, goals, off-chain safety, enforcement guarantees, node liquidity trust, assumptions, limitations, future improvements
static/img/protocol/state-ledger-advancement.png	copied unchanged from docs/protocol/state_ledger_advancement.png

Review updates

• Flattened current Protocol pages from docs/nitrolite/protocol/app-layer/*.mdx to docs/nitrolite/protocol/*.mdx.
• Removed the slug: /protocol/app-layer/overview override from the current overview.
• Updated Nitrolite/Clearnet inbound links and footer links to /nitrolite/protocol/introduction or the flattened page routes.
• Removed redundant sidebar_position frontmatter from explicit-sidebar current Protocol pages.
• Fixed canonical encoding wording from RLP to Solidity ABI encoding.
• Demoted reserved event messages from a full section to a note under Message Types.
• Removed the reviewed .mdx suffixes from versioned Markdown links.
• Adjusted Clearnet decentralized-layer category position from 5 to 4.
• Added AGENTS.md so future Docusaurus work runs typecheck/build, serves locally, fetches changed routes, and keeps internal doc links extensionless.

Adversarial source-only checks

• Searched current Nitrolite Protocol pages for @erc7824, @yellow-org/sdk, TypeScript, Go, Clearnet, Duck, v0.5, old VirtualApp/NitroRPC markers, and redundant visible v1 wording: no disallowed current Protocol hits.
• Searched migration separately: hits are source-backed by channel-protocol.md, cross-chain-and-assets.md, and terminology.md.
• Verified the source image is served from /img/protocol/state-ledger-advancement.png.
• Verified built current sidebar shows only App Layer and the nine planned pages.
• Verified built version dropdown maps current Protocol pages to /nitrolite/0.5.x/protocol/introduction when there is no exact 0.5.x equivalent, and maps 0.5.x Protocol introduction back to /nitrolite/protocol/introduction.
• Verified /clearnet/learn/decentralized-layer/overview remains available after conflict resolution.

Validation

• npm run typecheck passed.
• npm run build passed.
• npm run serve -- --host 127.0.0.1 --port 3014 passed.
• curl -fsS -L returned 200 for all nine current Protocol pages:
  • /nitrolite/protocol/introduction
  • /nitrolite/protocol/terminology
  • /nitrolite/protocol/cryptography-and-signing
  • /nitrolite/protocol/state-and-ledger-model
  • /nitrolite/protocol/channel-lifecycle
  • /nitrolite/protocol/enforcement-and-settlement
  • /nitrolite/protocol/cross-chain-and-assets
  • /nitrolite/protocol/interaction-model
  • /nitrolite/protocol/security-and-limitations
• curl -fsS -L also returned 200 for /nitrolite/0.5.x/protocol/introduction, /clearnet/learn/decentralized-layer/overview, and /img/protocol/state-ledger-advancement.png.

Build notes: Docusaurus still reports pre-existing/base broken links in Clearnet generated contract API pages and versioned 0.5.x pages, plus pre-existing broken anchors in versioned 0.5.x pages. No build failure remains, and the merge conflicts are resolved.

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[philanton]

Top-level structural suggestion

The 1.x Protocol tab is now App Layer-only. The nested protocol/app-layer/ directory adds a path segment that carries no information — every page already lives under the "Protocol" tab.

Move all pages from docs/nitrolite/protocol/app-layer/*.mdx up to docs/nitrolite/protocol/*.mdx. This also lets docs/nitrolite/protocol/introduction.mdx drop its slug: /protocol/app-layer/overview override and use a natural URL (or rename to protocol/overview.mdx). Removes the mixed sidebar id scheme between protocol/introduction and protocol/app-layer/*. Update sidebars-nitrolite.ts, the navbar docId in docusaurus.config.ts, and any inbound link in learn//build/ that already uses /nitrolite/protocol/app-layer/....

Cosmetic — duplicate ordering source

Each new App Layer page has sidebar_position: N in frontmatter, but the sidebar uses an explicit items: array — frontmatter positions are inert. Two sources of truth for ordering. Drop sidebar_position from the frontmatter, or switch the sidebar to autogenerated and rely on frontmatter alone. Pick one.

[ihsraham]

@philanton fixed the top-level notes. moved the pages up, removed the extra url override and ordering fields, updated the links, and checked the pages locally.

[philanton]

All review comments addressed in de19e21. RLP → Solidity ABI fix landed, .mdx suffixes dropped on versioned 0.5.x links, Clearnet category position reverted to 4, Event Messages stub collapsed to admonition, and the structural move flattened protocol/app-layer/* up to protocol/*. LGTM.