Add Serena configuration and project memories

(Set up Serena IDE integration with a Nix language server and create a
memory graph documenting package conventions, core structure, tech
stack, and task completion workflows.)

.serena/.gitignore

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+/cache
+/project.local.yml

.serena/memories/conventions.md

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+# nix-overlay — package conventions
+
+## Directory pattern (every package)
+`packages/<name>/default.nix` (wrapper, receives blueprint args) + `packages/<name>/package.nix` (the derivation, `pkgs.callPackage`-style argsets).
+
+Wrapper variants:
+- Plain: `{ pkgs, ... }: pkgs.callPackage ./package.nix { }`
+- Needs blueprint extras: pass `perSystem`, `inputs`, etc. through explicitly.
+- Alternate nixpkgs (freetoken): wrapper ignores `pkgs` for the derivation and calls `inputs.nixpkgs-torch211.legacyPackages.${pkgs.stdenv.hostPlatform.system}.callPackage ./package.nix { }`.
+
+## Derivedivation requirements
+- Use `stdenv.mkDerivation rec { pname; version; }` or `rustPlatform.buildRustPackage` (Rust: `cargoHash`; Go/Python equivalents as needed).
+- `meta.description` required (feeds the default meta-package listing).
+- `meta.mainProgram` set for CLI-providing packages.
+- Organizational attrs via `passthru`: `category` (e.g. "AI Coding Agents"), `hideFromDocs = true` to exclude from docs listing.
+- No `with pkgs;` at top level of Nix files (scope issues).
+- No hardcoded system paths/system assumptions.
+
+## Adding a package (sequence)
+mkdir → package.nix → default.nix wrapper → `git add packages/<name>/` (required for blueprint discovery) → `nix build .#<name>` → update README Available Packages table → commit (conventional-commit format).
+
+## Naming
+- Package dir name = flake output attr name (kebab-case).

.serena/memories/core.md

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+# nix-overlay — core
+
+Nix flake overlay (numtide/blueprint-based) exposing extra packages for Nix/NixOS.
+Repo: `git+https://git.millerson.name/alex/millerson-overlay.nix.git`
+
+## Source map
+- `flake.nix` — inputs + outputs; blueprint drives perSystem outputs; overlays/modules added manually on top.
+- `overlays/default.nix` — binary-cache-friendly: maps blueprint's pre-built `packages` under namespace `millerson-nix-overlay`.
+- `overlays/shared-nixpkgs.nix` — builds `packages/` tree against consumer's `final` via `mkPackagesFor`; shares deps, cache only hits on matching nixpkgs rev.
+- `packages/<name>/default.nix` + `package.nix` — every package follows this wrapper/derivation split. See `mem:conventions` for patterns.
+- `packages/default/` — meta-package; generates name\tdesc list from `perSystem.self`, filtering `passthru.hideFromDocs`.
+- `packages/flake-inputs/` — dummy derivation referencing all flake inputs so they get cached. `hideFromDocs = true`.
+- `treefmt.toml` — nixfmt for `*.nix`, flake.lock excluded.
+- `AGENTS.md` / `CLAUDE.md` — agent workflow rules (beads tracking, mandatory skills, caveman comms).
+
+## Project-wide invariants
+- All overlay packages live under the single attrset `millerson-nix-overlay` (not top-level attrs).
+- Blueprint discovers packages from the **git index**, not the working dir: new `packages/<name>/` must be `git add`-ed before `nix build .#<name>` sees it.
+- Three nixpkgs inputs; some packages deliberately build against non-default ones. See pins in `mem:tech_stack`.
+- Everything under `packages/` uses `pkgs.callPackage ./package.nix { }` wrapper pattern; `default.nix` receives blueprint args (pkgs, perSystem, inputs, ...).
+
+## Task workflow (from AGENTS.md, enforced)
+Runnable commands (build/format/update/bd/push): `mem:suggested_commands`. Exact done-checklist: `mem:task_completion`.
+
+
+- ALL task tracking via `bd` (beads): `bd ready`, `bd update <id> --claim`, `bd close <id>`. NEVER TodoWrite/markdown TODOs.
+- `bd prime` before starting work; `bd remember` for persistent knowledge (no MEMORY.md files).
+- Session not complete until `git push` succeeds (`bd dolt push` skipping with "No remote is configured" is expected, not a failure).
+- Commits use conventional-commit format.
+- For nixpkgs/option lookups use the `nix` skill; for flake/devShell ops the `nix-flakes` skill; comms in caveman mode.

.serena/memories/memory_maintenance.md

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+# Memory Maintenance
+
+## Discovery Model
+
+- Core principle: progressive discovery through references, building a graph of memories.
+- Initially, agents are provided with the list of all memories (names only).
+- Agents should read `mem:core` as the top-level entry point (graph root).
+  This memory should contain references to other memories covering major project domains.
+  The referenced memories shall, in turn, shall contain references to even more specific memories, and so on.
+  The depth of the graph shall depend on the project complexity.
+- Use topics/folders to group related memories in order to make the content structure explicit.
+  Folders can mirror project structure (e.g. modules like frontend/backend) or topics like debugging, architecture, etc.
+- Memory references must use a mem: prefix inside backticks, e.g. `mem:frontend/core`.
+  The surrounding text should clearly indicate when to read the memory/which content to expect.
+  The text should provide more precise guidance than the memory name alone, 
+  i.e. avoid a reference like "frontend debugging: `mem:frontend/debugging` and instead make clear which aspects of frontend debugging are covered.
+- Memories themselves should not contain information about when to read them; this is the responsibility of the referring memory.
+
+## Style
+
+Dense agent notes, not prose docs. Prefer invariants, terse bullets. 
+Avoid obvious context, rationale, and examples unless they prevent likely mistakes. 
+Keep guidance durable and generalizable, not task-local.
+
+## Add/update threshold
+
+Add or update memories only with stable, non-obvious project conventions that avoid complex rediscovery in the future.
+Do not add: quick-read facts; generic language/framework knowledge; one-off task notes; volatile line-level details; behavior likely to change soon.
+
+## Maintenance Actions
+
+- Renaming memories: References are updated automatically if handled via Serena's memory rename tool.
+- Checking for stale memories (e.g. after deletion): Call `serena memories check` for a report.

.serena/memories/suggested_commands.md

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+# nix-overlay — commands
+
+All run from repo root (`nix-overlay/`).
+
+## Build / run
+- `nix build .#<package>` — build one package (must be `git add`-ed first if new; blueprint reads git index).
+- `nix run .#<package>` — run a package CLI (needs `meta.mainProgram`).
+- `nix build .#default` — build the meta-package (package listing).
+- `nix flake show` — inspect flake outputs (also index-limited).
+- `nix flake check` — full check incl. formatting.
+- `nix develop` — dev shell from blueprint.
+
+## Format
+- `nix fmt` (treefmt → nixfmt on *.nix). Same as `nix flake check`'s format gate.
+
+## Package updates
+- `nix-update <package>` — bump version + hashes (cargoHash etc.).
+- `nix-update <package> --version <v>` — specific version.
+- `nix-update skillsmcp --version=branch=main` — for commit-pinned pkgs; or `--commit <sha>`.
+
+## Beads (mandatory task tracking)
+- `bd prime` — session context, run before any work.
+- `bd ready` / `bd show <id>` / `bd update <id> --claim` / `bd close <id>`.
+- `bd remember` — persistent knowledge instead of MEMORY.md.
+- `bd dolt push` — prints "No remote is configured — skipping." (expected; exit 0).
+
+## Session completion push
+```
+git pull --rebase && bd dolt push && git push
+git status  # must show "up to date with origin"
+```
+
+## Serena
+- `serena memories check` — verify memory references after edits/deletes.

.serena/memories/task_completion.md

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+# nix-overlay — task completion
+
+Done when ALL of these pass/hold:
+
+1. Build passes: `nix build .#<package>` (or `nix flake check` for cross-cutting changes). Never leave a package committed that doesn't build.
+2. Formatting: `nix fmt` clean (nixfmt; `flake.lock` excluded).
+3. New package is staged (`git add packages/<name>/`) before build — blueprint index requirement.
+4. README.md Available Packages table updated if package added/changed visibly.
+5. Commit: conventional commit format (use conventional-commit / caveman-commit skill). No work left uncommitted.
+6. Beads: work claimed via `bd update <id> --claim` before, `bd close <id>` after.
+7. Pushed: `git pull --rebase && bd dolt push && git push` then `git status` shows "up to date with origin". `bd dolt push` skip message is expected, not a failure. Do not stop before push succeeds.

.serena/memories/tech_stack.md

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+# nix-overlay — tech stack
+
+- Language: Nix. Build system: Nix flake via `numtide/blueprint` (with `flake-parts`, `systems` for multi-system).
+- Formatting: `treefmt-nix` → `nixfmt` on `*.nix` (`flake.lock` excluded in `treefmt.toml`).
+- Multi-input nixpkgs setup (flake.nix) — pins matter, do not "unify" them:
+  - `nixpkgs` = nixos-unstable (default; blueprint follows it).
+  - `nixpkgs-latest` = nixos-unstable — needed by packages requiring newer toolchains: rustc >= 1.95 (mcp-gateway >= 3.4.0), go >= 1.26.3 (kubernetes-mcp-server >= 0.0.66).
+  - `nixpkgs-torch211` = pinned rev `549bd84d6279f9852cae6225e372cc67fb91a4c1` — freetoken pins torch>=2.11,<2.12 / triton==3.6.0; nixos-unstable ships torch 2.13/triton 3.7, so freetoken builds via `inputs.nixpkgs-torch211.legacyPackages.${system}.callPackage` (see `packages/freetoken/default.nix`).
+  - `bun2nix` pinned to branch `staging-2.1.0` until catalog support (bun2nix#86) lands on default branch (TODO #4001).
+- Package kinds in `packages/`: mostly Rust (rustPlatform.buildRustPackage), Go, Python/torch, Node/bun; each self-contained in its own dir.
+- `flake.lock` managed only via `nix flake update` — never hand-edited.

.serena/project.yml

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+# the name by which the project can be referenced within Serena/when chatting with the LLM.
+project_name: "nix-overlay"
+
+# list of language servers to start when using the LSP backend; choose from:
+#   ada                    al                     angular                ansible                bash
+#   bsl                    clojure                cpp                    cpp_ccls               crystal
+#   csharp                 csharp_omnisharp       cue                    dart                   deno
+#   elixir                 elm                    erlang                 fortran                fsharp
+#   gdscript               gleam                  go                     groovy                 haskell
+#   haxe                   hlsl                   html                   java                   json
+#   julia                  kotlin                 latex                  lean4                  lua
+#   luau                   markdown               matlab                 msl                    nextflow
+#   nix                    ocaml                  pascal                 perl                   php
+#   php_phpactor           php_phpantom           powershell             python                 python_basedpyright
+#   python_jedi            python_pyrefly         python_ty              qml                    r
+#   rego                   ruby                   ruby_solargraph        rust                   scala
+#   scss                   solidity               svelte                 swift                  systemverilog
+#   terraform              toml                   typescript             typescript_vts         vue
+#   wolfram                yaml                   zig
+#   (This list may be outdated; generated with scripts/print_language_list.py;
+#   For the current list, see values of the LanguageServerId enum here:
+#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
+# For some languages, there are several alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
+# Note:
+#   - For C, use cpp
+#   - For JavaScript, use typescript
+#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
+#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
+#   - For Deno projects, use deno (serves the same .ts/.js files as typescript; requires the deno CLI on PATH)
+#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
+#   - For Free Pascal/Lazarus, use pascal
+# Special requirements:
+#   Some language servers require additional setup/installations.
+#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
+# When using multiple language servers, the first language server that supports a given file will be used for that file.
+# The first language server is the default language and the respective language server will be used as a fallback.
+# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
+language_servers:
+- nix
+
+# the encoding used by text files in the project
+# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
+encoding: "utf-8"
+
+# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
+# the command runs in the project root directory and is only executed if the project is trusted
+# (see trusted_project_path_patterns in the global configuration).
+# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
+# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
+# backstop for non-terminating commands; on expiry the process is killed and activation continues.
+# example: activation_command: "npx nx run-many -t build"
+activation_command:
+
+# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
+# must be a positive number.
+activation_command_timeout: 180.0
+
+# line ending convention to use when writing source files.
+# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
+# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
+line_ending:
+
+# The language backend to use for this project.
+# If not set, the global setting from serena_config.yml is used.
+# Valid values: LSP, JetBrains
+# Note: the backend is fixed at startup. If a project with a different backend
+# is activated post-init, an error will be returned.
+language_backend:
+
+# whether to use project's .gitignore files to ignore files
+ignore_all_files_in_gitignore: true
+
+# advanced configuration option allowing to configure language server-specific options.
+# Maps the language key to the options.
+# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
+ls_specific_settings: {}
+
+# list of workspace folder paths (LSP backend only).
+# These folders will be used to build up Serena's symbol index.
+# Paths must be within the project root and should thus be relative to the project root.
+# Furthermore, the paths should not be filtered by ignore settings.
+# Default setting: The entire project root folder (".") is considered.
+# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
+#   ls_workspace_folders:
+#     - "./subproject1"
+#     - "./subproject2"
+ls_workspace_folders:
+- "."
+
+# list of additional workspace folder paths for cross-package reference support.
+# Paths can be absolute or relative to the project root.
+# Each folder is registered as an LSP workspace folder, enabling language servers to discover
+# symbols and references across package boundaries, but these folders are not indexed by Serena,
+# i.e. the respective symbols will not be found using Serena's symbol search tools.
+# Example:
+#   additional_workspace_folders:
+#     - ../sibling-package
+#     - ../shared-lib
+ls_additional_workspace_folders: []
+
+# list of additional paths to ignore in this project.
+# Same syntax as gitignore, so you can use * and **.
+# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases.
+# Example:
+#   ignored_paths:
+#     - "examples/**"
+#     - ".worktrees/**"
+#     - "**/bin/**"
+#     - "**/obj/**"
+# Note: global ignored_paths from serena_config.yml are also applied additively.
+ignored_paths: []
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+# list of tool names to exclude.
+# This extends the existing exclusions (e.g. from the global configuration)
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+excluded_tools: []
+
+# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
+# This extends the existing inclusions (e.g. from the global configuration).
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+included_optional_tools: []
+
+# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
+# This cannot be combined with non-empty excluded_tools or included_optional_tools.
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+fixed_tools: []
+
+# list of mode names that are to be activated by default, overriding the setting in the global configuration.
+# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
+# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
+# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
+# for this project.
+# This setting can, in turn, be overridden by CLI parameters (--mode).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
+default_modes:
+
+# list of mode names to be activated additionally for this project, e.g. ["query-projects"]
+# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
+added_modes:
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ""
+
+# time budget (seconds) per tool call for the retrieval of additional symbol information
+# such as docstrings or parameter information.
+# This overrides the corresponding setting in the global configuration; see the documentation there.
+# If null or missing, use the setting from the global configuration.
+symbol_info_budget:
+
+# list of regex patterns which, when matched, mark a memory entry as read‑only.
+# Extends the list from the global configuration, merging the two lists.
+read_only_memory_patterns: []
+
+# list of regex patterns for memories to completely ignore.
+# Matching memories will not appear in list_memories or activate_project output
+# and cannot be accessed via read_memory or write_memory.
+# To access ignored memory files, use the read_file tool on the raw file path.
+# Extends the list from the global configuration, merging the two lists.
+# Example: ["_archive/.*", "_episodes/.*"]
+ignored_memory_patterns: []