codebase-memory-mcp: consume the kriswill nix fork instead of the sub-flake

[kriswill]

Summary

Replaces the in-repo flakes/codebase-memory-mcp/ sub-flake (which fetched a pinned DeusData release tag and applied patches at build time) with our kriswill/codebase-memory-mcp nix fork consumed as a GitHub flake input.

The fork branch tracks upstream (DeusData) main and carries all the Nix work directly in the source, which unlocks three wins: we track upstream changes via git, we keep all of upstream's existing tooling + our Nix build advantages, and the cbm index now lives in that codebase so it can enhance work on itself.

Supersedes #18 (the patch-based sub-flake approach).

The fork branch

github:kriswill/codebase-memory-mcp/nix (3 commits on upstream/main):

• Nix symbol extraction — source_expression→source_code fix + walk_nix_bindings (bindings → Variables named by attrpath) + Nix in walk_defs descend. (Upstream had already merged the function_expression naming, so only the still-missing half was ported.)
• Flake-topology passes — pass_flakelock.c (flake.lock → Flake + DEPENDS_ON/FOLLOWS/MOUNTS, via the already-vendored yyjson, no Nix eval) and pass_nix_eval.c (nix flake show --json → FlakeOutput + PRODUCES, failure-tolerant + timeout-bounded).
• Nix packaging — cbm-with-ui build (graph-ui embedded), nix/git/coreutils wrapper, cbm-tools (cbm-ctl/cbm-daemon), and the darwinModules.codebase-memory-mcp launchd module — all in the fork's flake.nix + nix/.

What changed here

• flake.nix: input codebase-memory-mcp.url → github:kriswill/codebase-memory-mcp/nix (dropped the now-absent flake-parts follows).
• Removed flakes/codebase-memory-mcp/ (moved into the fork).
• modules/{packages,overlays}.nix + modules/darwin/codebase-memory-mcp.nix: comment refresh only — the attr names (packages.<sys>.codebase-memory-mcp, darwinModules.codebase-memory-mcp) are unchanged, so the re-export wiring is untouched.

Verification

• nix eval .#packages.aarch64-darwin.codebase-memory-mcp.name → codebase-memory-mcp-0.8.1-nix
• nix eval .#darwinConfigurations.k.config.kriswill.codebase-memory.enable → true
• launchd ProgramArguments → …-cbm-tools-0.8.1-nix/bin/cbm-daemon
• nix build .#packages.aarch64-darwin.codebase-memory-mcp (via the fork input, under dotfiles' nixpkgs)
• Fork branch independently verified: flake.lock topology edges, Nix symbols, resolved outputs (on a synthetic flake)

Follow-up

• Phase 3 (option define↔set CONFIGURES linker) can now be developed in the fork with the cbm index available for the work.