chore(beads): close package update task

Record the completed package bumps and the freetoken 0.2.0 blocker.

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Co-Authored-By: Codebuff <noreply@codebuff.com>

.beads/issues.jsonl

@@ -14,6 +14,7 @@
 {"_type":"issue","id":"nix-overlay-a9m","title":"Fix haivemind startup after MainScreen mount","description":"Restore deferred engine startup while preserving MainScreen widget lookup fix.","status":"closed","priority":1,"issue_type":"bug","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-20T11:20:36Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-20T11:21:43Z","started_at":"2026-08-20T11:20:43Z","closed_at":"2026-08-20T11:21:43Z","close_reason":"Restored engine startup after MainScreen mount and verified package build.","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-bjd","title":"Add nftables-analyzer CLI package","description":"Add python3Packages.buildPythonApplication derivation for reinaldosaraiva/nftables-analyzer (CLI only). Pin to main commit 5fc78d0c9ce173e3baa80a5655bcadb1b2f78493 (no tags upstream). sourceRoot=source/backend, hatchling build system. Category: Networking. Frontend excluded - upstream repo missing frontend/src/lib modules.","status":"closed","priority":2,"issue_type":"task","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-07T04:48:07Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-07T04:50:25Z","started_at":"2026-08-07T04:48:10Z","closed_at":"2026-08-07T04:50:25Z","close_reason":"Package added, built, smoke-tested, committed","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-bju","title":"codeaf: build furrow from source instead of embedding the upstream release binary","description":"The codeaf package embeds the upstream Agent-Field/furrow release asset (fetchurl -\u003e cmd/fetch -from -\u003e go:embed). Those bytes are glibc-dynamic and never patched, so the copy codeaf extracts to ~/.codeaf/bin/furrow-0.1.0 dies on NixOS with 'Could not start dynamically linked executable ... stub-ld'. Build furrow (Rust, Apache-2.0, same version as internal/furrowbin/pin.json) from source in this overlay and hand it to codeaf through CODEAF_FURROW, which internal/furrow lookBinary prefers over the embedded copy.","status":"closed","priority":2,"issue_type":"task","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-10-07T07:44:58Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-10-07T08:33:54Z","started_at":"2026-10-07T07:45:20Z","closed_at":"2026-10-07T08:33:54Z","close_reason":"Shipped in ff1fecc0edc4: packages/codeaf/furrow.nix builds furrow 0.1.0 from source, codeaf wraps its binary with CODEAF_FURROW and no longer stages the upstream release asset.","dependency_count":0,"dependent_count":0,"comment_count":0}
+{"id":"nix-overlay-c5y","title":"chore: update packages to latest upstream versions","description":"Bump all packages in packages/ to their latest upstream release where appropriate; recompute source/npm/cargo hashes and verify builds.","status":"closed","priority":2,"issue_type":"chore","assignee":"minder","created_at":"2026-10-24T08:00:40.304835399Z","created_by":"minder","updated_at":"2026-10-24T11:10:02.842081264Z","closed_at":"2026-10-24T11:10:02.830616733Z","close_reason":"Bumped all stale packages (awg-tool, awgen, codeaf, ds4, freebuff, graphify, hipengine, kubernetes-mcp-server, kyojin, marmel, omniroute, open-code-review, pilotdeck, radar, traycer), removed llama-cpp, and verified every bumped package with nix build; kyojin.tests.jit passes. Remaining packages are already current; freetoken 0.2.0 stays blocked on newer torch (nix-overlay-qcg).","source_repo":"nix-overlay","compaction_level":0,"original_size":0}
 {"_type":"issue","id":"nix-overlay-du9","title":"Add kyojin package (Yamz-Labs/kyojin, ExLlamaV3 fork for Strix Halo)","description":"Package https://github.com/Yamz-Labs/kyojin: Yamz inference engine, a fork of ExLlamaV3 targeting AMD Strix Halo (gfx1151) on ROCm 7. Build the python package with the ROCm build of torch from nixpkgs and compile the HIP extension for gfx1151.","notes":"re-pinned to release tag v1.3 (latest GitHub release; v1.1 was stale), version = \"1.3\", updateScript uses tags; rebuilt from v1.3 sources, wrappers --help verified","status":"closed","priority":2,"issue_type":"feature","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-10-07T08:44:23Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-10-07T15:14:30Z","started_at":"2026-10-07T08:49:12Z","closed_at":"2026-10-07T15:14:30Z","close_reason":"Closed","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-dv3","title":"Fix Config screen crash on F2","description":"F2 opens ConfigScreen then Textual raises InvalidSelectValueError because _refresh_aggregator_dropdown assigns Select.BLANK, resolved as False, instead of clearing selection.\\n\\nAcceptance: Config screen opens with saved consensus configuration; regression covers no selected aggregator; targeted tests pass.","status":"closed","priority":1,"issue_type":"bug","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-20T11:34:03Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-20T11:37:47Z","started_at":"2026-08-20T11:34:07Z","closed_at":"2026-08-20T11:37:47Z","close_reason":"Replaced invalid Select.BLANK handling; built haivemind and verified ConfigScreen headlessly.","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-ez7","title":"marmel: Landlock sandbox-exec tests fail in the Nix build sandbox","description":"Both harness::sandbox::tests::test_internal_sandbox_* tests re-exec sh through marmel --internal-sandbox-exec. Upstream apply_landlock_linux() allow-lists FHS paths only (/usr /bin /lib /opt /etc /var ...), never /nix/store, and PathFd() silently skips paths missing in the sandbox. Inside the Nix sandbox PATH points at /nix/store/-bash/bin and /nix/store/-coreutils/bin, so exec is denied: 'Failed to exec shell in sandbox: Permission denied (os error 13)'. Not a code defect: on a real NixOS host sh resolves through /bin -\u003e system path which the /bin rule covers.","status":"closed","priority":2,"issue_type":"task","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-10-06T18:58:44Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-10-06T19:31:56Z","started_at":"2026-10-06T18:59:02Z","closed_at":"2026-10-06T19:31:56Z","close_reason":"Skipped both sandbox-exec tests in packages/marmel; nix build .#marmel green (342/344 run). Runtime defect split out to nix-overlay-5ml.","dependency_count":0,"dependent_count":0,"comment_count":0}
@@ -27,5 +28,6 @@
 {"_type":"issue","id":"nix-overlay-pnb","title":"marmel: drop landlock-nix-store.patch once upstream allows /nix/store (Na1w/marmel#14)","description":"packages/marmel/landlock-nix-store.patch adds \"/nix/store\" to the read-only+execute allow-list (ro_paths, src/harness/sandbox.rs:417). Upstream allow-lists FHS paths only, and every executable on a Nix host resolves below the store, so the Landlock re-entry cannot exec `sh` and each shell tool call returns \"Failed to exec shell in sandbox: Permission denied (os error 13)\" with exit 1. Filed upstream as https://github.com/Na1w/marmel/issues/14 (open, 2026-10-16).\n\nWhen upstream takes a store path: bump the package, delete the patch, and check the sandbox tests in the build log. test_internal_sandbox_cross_directory_rename must still run (no SKIP line from integration_host) and pass; test_internal_sandbox_exec_dev_null_and_dns stays filtered for its own reason, the no-network build sandbox has no /etc/resolv.conf. Local history: nix-overlay-5ml (closed), fix commit 51dd95c19c18.","status":"open","priority":3,"issue_type":"task","owner":"alex@millerson.name","created_at":"2026-10-16T13:23:24Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-10-16T13:23:24Z","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-q00","title":"Add haivemind package","description":"Package https://github.com/dev-boz/haivemind in the Nix overlay, document it, validate the build, and complete repository workflow.","status":"closed","priority":2,"issue_type":"task","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-08T16:32:37Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-08T16:36:41Z","started_at":"2026-08-08T16:33:00Z","closed_at":"2026-08-08T16:36:41Z","close_reason":"Closed","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-q2m","title":"Add FreeToken package (FlashML-org/FreeToken)","description":"Package https://github.com/FlashML-org/FreeToken into the overlay following the standard packages/\u0026lt;name\u0026gt;/{default.nix,package.nix} pattern. Must build via nix build, README updated, category set.","notes":"Build in progress. Resolved: tvm-ffi 0.1.13.post3 builds (cython 3.3.0 vendored, dontUsePytestCheck due to xdist addopts), flashlib wheel + pythonRemoveDeps, freetoken pythonRelaxDeps gguf/modelscope. Remaining: torch-bin CUDA closure (nccl done; libnvshmem source build ~hours), then freetoken extensions. Note: torch-bin 2.11 = +cu128 PyPI wheel autoPatchelf'd to nixpkgs cuda12.9 libs.","status":"closed","priority":2,"issue_type":"feature","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-30T06:40:20Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-30T17:51:10Z","started_at":"2026-08-30T06:40:34Z","closed_at":"2026-08-30T17:51:10Z","close_reason":"freetoken 0.1.2 packaged: builds via nix build .#freetoken, ft CLI verified (ft --version), imports checked, RPATHs correct (cudart 12.9 + torch-bin libs). Docs in README + meta.longDescription.","dependency_count":0,"dependent_count":0,"comment_count":0}
+{"id":"nix-overlay-qcg","title":"freetoken: bump 0.1.3 -> 0.2.0 once nixpkgs has torch 2.14 / transformers 5.18","description":"FreeToken 0.2.0 requires torch>=2.14,<2.15, torchvision>=0.29,<0.30, transformers>=5.18,<5.19, triton 3.8 and flashlib==0.4.0 (currently packaged: 0.3.0). nixos-unstable ships torch 2.11 and transformers 5.5.4, so the pin in flake.nix (nixpkgs-torch211) and packages/freetoken/package.nix must be reworked once a newer torch lands in nixpkgs.","status":"open","priority":3,"issue_type":"task","created_at":"2026-10-24T09:01:39.154532688Z","created_by":"minder","updated_at":"2026-10-24T09:01:39.154532688Z","source_repo":"nix-overlay","compaction_level":0,"original_size":0}
 {"_type":"issue","id":"nix-overlay-vhq","title":"Note missing Dolt remote in AGENTS.md","description":"## Why\\nAgents running bd dolt push see 'No remote is configured - skipping' and may mistake it for a failure (blocking session close). Document that this is expected: no Dolt remote is set up, beads state is versioned locally in .beads/ and committed via git.\\n\\n## What\\nAdd a short note in the Beads Issue Tracker / Session Completion section of AGENTS.md.\\n\\n## Acceptance\\n- AGENTS.md explains the expected bd dolt push output and that git push is the actual sync mechanism","status":"closed","priority":3,"issue_type":"task","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-08-07T13:18:33Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-08-07T13:19:26Z","started_at":"2026-08-07T13:18:51Z","closed_at":"2026-08-07T13:19:26Z","close_reason":"AGENTS.md updated and pushed","dependency_count":0,"dependent_count":0,"comment_count":0}
 {"_type":"issue","id":"nix-overlay-ylf","title":"Add open-code-review package","description":"Package alibaba/open-code-review (AI code review CLI, npm @alibaba-group/open-code-review) into the overlay","status":"closed","priority":2,"issue_type":"feature","assignee":"Alexander Miroshnichenko","owner":"alex@millerson.name","created_at":"2026-09-26T07:18:05Z","created_by":"Alexander Miroshnichenko","updated_at":"2026-09-26T07:24:49Z","started_at":"2026-09-26T07:18:48Z","closed_at":"2026-09-26T07:24:49Z","close_reason":"Closed","dependency_count":0,"dependent_count":0,"comment_count":0}