docs: Align verification guidance to prefer nix flake check

Replace broad direct Cargo verification guidance with repository-level
`nix flake check` across AGENTS.md, durable context files, and bash-policy
examples. Preserves `cargo fmt` for explicit autofix formatting flows.

Co-authored-by: SCE <sce@crocoder.dev>

Author: davidabram

.sce/config.json

@@ -27,7 +27,7 @@
               "--check"
             ]
           },
-          "message": "This repository prefers `nix flake check` over direct `cargo fmt --check`. Run `nix flake check` instead."
+          "message": "This repository prefers `nix flake check` over direct `cargo fmt --check`. Run `nix flake check` for verification; keep `cargo fmt` for autofix-only formatting."
         }
       ]
     }

AGENTS.md

@@ -50,13 +50,13 @@ Run these through Nix from repo root unless noted otherwise.
 - Run CLI: `nix develop -c sh -c 'cd cli && cargo run -- --help'`
 - Build packaged CLI output: `nix build .#default`
 - Run packaged CLI app: `nix run .#sce -- --help`
-- Run all CLI tests: `nix develop -c sh -c 'cd cli && cargo test'`
-- Run a single test by exact name: `nix develop -c sh -c 'cd cli && cargo test parser_routes_mcp -- --exact'`
-- Run tests in one module/file pattern: `nix develop -c sh -c 'cd cli && cargo test setup'`
+- Preferred repo-level verification: `nix flake check`
+- Run a single Rust test by exact name when explicitly needed: `nix develop -c sh -c 'cd cli && cargo test parser_routes_mcp -- --exact'`
+- Run Rust tests in one module/file pattern when explicitly needed: `nix develop -c sh -c 'cd cli && cargo test setup'`
 - Run ignored? none were found; do not assume ignored-test flows exist.
-- Format check: `nix develop -c sh -c 'cd cli && cargo fmt --check'`
+- Rust format verification is covered by `nix flake check`
 - Auto-format: `nix develop -c sh -c 'cd cli && cargo fmt'`
-- Lint: `nix develop -c sh -c 'cd cli && cargo clippy --all-targets --all-features'`
+- Rust lint verification is covered by `nix flake check`
 
 ### Bun config/plugin commands