docs: update Aggregation Mode and deprecate Verification Layer

[JuArce]

Closes #2305

Why

The Aligned Verification Layer is deprecated and Aggregation Mode is the only active system in this repo, but the docs still presented both as live products — and in places recommended starting with the Verification Layer. The Aggregation Mode pages were also stale: two of them still told users it lived on the staging branch.

Approach: archive, don't delete

Verification Layer pages move to docs/archive/ rather than being removed. The archive mirrors the original directory depth, so the relative image links inside moved pages keep resolving with no edits. Archived pages are not listed in SUMMARY.md, so GitBook stops showing them in the nav while they stay reachable by URL.

Operator guides stay where they are, with a deprecation banner, and are dropped from SUMMARY.md so they no longer appear in the GitBook.

Surviving guide filenames are not renumbered — GitBook orders the nav from SUMMARY.md, and renaming would break published docs.alignedlayer.com URLs.

Aggregation Mode fixes

Beyond removing the staging branch instructions, these were verified against a release build of agg_mode_cli:

• agg_mode_cli --version does not exist. The CLI declares no version flag, so the documented install check errored. Replaced with --help.
• Binary name was wrong in two places — agg-mode-cli vs the real agg_mode_cli.
• deposit sends a fixed 0.0035 ether, not an arbitrary amount. This was undocumented.
• --public-inputs was documented as optional but verify-on-chain exits with Public input file not provided without it.
• --proving-system Risc0 is accepted by the parser but the check is always performed as SP1. Documented as non-functional rather than dropped, since --help still advertises it.
• SDK reference had no install section. Added install + Hello World, plus the missing Risc0 variant of AggregationModeVerificationData. No released tag contains agg_mode_sdk (at v0.20.0 the aggregation_mode/ tree has no sdk/ crate), so the dependency pins branch = "testnet" — confirmed to resolve.
• The L2 example guide no longer routes step 1 through the Verification Layer, and make batcher_start_ethereum_package is gone from its localnet setup. The example code already depended only on agg_mode_sdk; only the prose was stale. Same fixes applied to examples/l2/README.md.

Rewrites

• Try Aligned is now an Aggregation Mode quickstart, using the SP1 test proof already in scripts/test_files/sp1/.
• Generating proofs covers SP1 compressed proofs and the four artifacts the CLI needs, derived from fibonacci_proof_generator.
• Key Terms and Supported Verifiers describe the aggregation pipeline instead of the AVS.
• New Explorer page under the Proof Aggregation Service, documenting the aggregated proof views (written from the LiveView templates — no invented screenshots).
• About Aligned, Use cases, FAQ, Why ZK lose the "choose between two modes" framing.

Unrelated bugs fixed along the way

• Hoodi AlignedProofAggregationService was listed twice with different addresses. Kept the one matching aggregation_mode/sdk/src/constants.rs and the deployment output (0x6B34AAaE…).
• Noted that the CLI and SDK do not support Sepolia ("0x0" address, empty gateway URL).
• RaaS Figure 1 was repointed to the wrong image by Docs update use cases 20250905 #2111, which left Figure 2 dangling on a file renamed in that same commit. Both correct now.
• The ansible runbook said mainnet tracks main, but both ini configs set git_branch=staging — and main does not exist on the remote.

Verification

• Relative link/image check across all of docs/: 41 broken → 3, the 3 remaining being pre-existing breaks in docs/0_internal/ (left alone, unpublished internal runbooks).
• No batcher, Proof Verification Layer, aligned submit, agg-mode-cli or checkout staging left in published docs.
• Every make target and file path referenced by published docs confirmed to exist.
• Every documented CLI flag checked against --help on a real release build.
• GitBook hint blocks and code fences balanced in every file.
• External link checker run; no new dead links.

Follow-ups (code, not docs)

• verify-on-chain ignores --proving-system and always builds AggregationModeVerificationData::SP1.
• deposit's clap help string says "Send 1 ether" but it sends 0.0035.

🤖 Generated with Claude Code

[github-actions]

Codex Code Review

• Low — Broken setup links after moving the guide. Moving the guide to docs/archive/3_guides/6_setup_aligned.md breaks existing links in the Circom, validating-public-input, and ZkQuiz example READMEs. Update those links to the archive location.

No security vulnerabilities or significant performance issues found in this documentation-only diff.

[claude]

Review

This is a docs-only PR (no application/contract code changes), so the security/perf/logic-bug categories mostly don't apply. I focused on factual accuracy and link integrity instead.

Verified and looks solid:

• All archived-page relative links (images, cross-references) correctly account for the extra directory depth from moving into docs/archive/ (e.g. 2_architecture/components/3_service_manager_contract.md's contract link goes from ../../../ to ../../../../).
• Operator guides now point to ../archive/3_guides/8_contract_addresses.md for the (deprecated) strategies list — correct path, previously pointed to a non-existent 7_contract_addresses.md.
• CLI flags/commands cross-checked against the actual Makefile targets (agg_mode_gateway_start_ethereum_package, agg_mode_payments_poller_start_ethereum_package, agg_mode_install_cli) — all exist.
• vk.hash_bytes() used in the new "Generating Proofs" guide matches the real usage in scripts/test_files/sp1/fibonacci_proof_generator/script/src/main.rs.
• File paths used in the rewritten "Try Aligned" quickstart (sp1_fibonacci_5_0_0.proof, _vk.bin, .vk, .pub) all exist under scripts/test_files/sp1/.
• Grepped for leftover stale references (batcher_start_ethereum_package, checkout staging, agg-mode-cli, aligned submit, links to the old Verification Layer page) outside docs/archive/ — none found.

No bugs or inaccuracies found. The archive-vs-delete approach, deprecation banners, and SUMMARY.md pruning are all consistent and correctly cross-linked. Nice thorough verification pass in the PR description itself (link checker, flag-by-flag --help checks).

No inline comments needed — nothing rose to the level of a real defect.

[JuArce]

/claude /codex

[github-actions]

Codex Code Review

No actionable issues found in the PR diff. The changes are documentation-only; no security vulnerabilities or significant performance issues were identified.