Tighten repo layout for ix agents and benches

[Andrew Gazelka (andrewgazelka)]

Summary

• remove the exported templates.ix flake template and point docs at direct mkDev composition
• move bench/filesystem to packages/indexbench/filesystem while keeping .#bench-filesystem
• refresh README layout guidance so skills and package-owned assets live under packages/ and lib/ is shared API only

Fixes #1519

Validation

• nix fmt flake.nix packages/indexbench/filesystem/default.nix examples/dev-fleet/default.nix
• nix eval --json .#templates
• nix build .#bench-filesystem --no-link
• nix flake show --json failed on this aarch64-darwin host while evaluating x86_64-linux checks because no remote x86_64-linux builder was available.

(sent by an AI agent via Claude Code)

Note

Reorganize repo layout by consolidating packages under packages/

• Moves bench/filesystem/ to packages/indexbench/filesystem/, sdk/ to packages/sdk/, and maintainers/scripts/ to packages/maintainers/scripts/, with no content changes to the moved files.
• Updates flake.nix input paths and tool script references to resolve under the new packages/ layout; removes the templates.ix flake output and the templates/ix/ directory entirely.
• Updates internal doc comments, error messages, and path references across the codebase to reflect the new locations.

^{Macroscope summarized 3ade5b4.}

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