# Workflow system execution

Source: [`../workflow-discovery.md`](../workflow-discovery.md)

Apply the global and repository-local `AGENTS.md` files and the ponytail skill
at full intensity throughout. Preserve user work, prefer native capabilities,
and add no abstraction without a demonstrated repeated need.

## Non-negotiable activation boundary

Only the user may switch or activate configurations. The agent must never run
`nixos-rebuild switch`, a Home Manager activation or switch command, or any
equivalent operation that changes the active generation. Building and
evaluating configurations is allowed; after a successful build, give the user
the exact activation command and wait for confirmation.

On 2026-09-05 the agent violated this boundary by directly running a built Home
Manager activation package. It restarted the Kitty service and closed the
user's terminal session. Do not repeat this, including for changes described as
user-level, harmless, temporary, or needed only for live verification.

## Current checkpoint

- Tranche: desktop, agents, and notes
- State: Walker and notes verified; ready for the first bounded Herdr pilot
- Branch: `chore/workflow-system`
- Baseline: `nix flake check --no-build --quiet` and a no-link Zenith system
  build passed on 2026-09-05 with the project-root launcher change and restart
  trigger removal; only the expected dirty-tree and unknown `modules` warnings
  were emitted. The generated project menu finds 30 live repositories without
  `.archive` or `.worktrees` entries, and the generated daily-note configuration
  passes an isolated same-day idempotence test. The managed Actual and WhatsApp
  entries are active in the current user session, Evolution's source registry
  activates over D-Bus, and the VPN reconnects successfully. The user activated the
  terminal root fix: `xdg-terminal-exec` now selects Kitty correctly and Yazi
  launches from Walker. After restarting the stale Elephant and Walker
  processes, repository launch also succeeds and exiting Neovim leaves a shell
  in the repository. The daily-note launcher and migrated notebook contents
  also pass their live sanity check. The attempted Elephant menu restart trigger
  stopped its dependent Walker during activation without bringing Walker back,
  so it has been removed in favor of applying rare menu changes at login. After
  activating that removal and relogging, Walker opens normally and repository
  selection starts Neovim in Oil at the project root.
- Next: use Herdr for one read-only fresh-session resume check, including agent
  state detection and detach/reattach, before adding any Herdr configuration.

## Progress

| Batch | State | Evidence or blocker |
| --- | --- | --- |
| Bootstrap and repository ownership | Waiting for user | Repository and dashboard reconciliation complete; credential cleanup remains |
| Declarative workstation foundation | Complete | All-host builds pass with one Nixpkgs pin, `just`, and an explicit Podman Compose provider |
| Repository contracts and workbench | Waiting externally | Three contracts and read-only Kubernetes pass; API deployment/access evidence is externally blocked, while database/report scaffolding is deferred until a real investigation |
| Desktop navigation and interaction | Active | Walker project and terminal actions plus stable Actual/WhatsApp launchers work; Outlook and two-output checks remain |
| Agent workflow | Active | The `nixos-maintainer` skill validates and builds; Herdr 0.8.2 is installed with only native state and awaits its first bounded live check |
| Notes | Complete | The daily launcher and migrated notebook pass live checks; the approved rollback copy is recoverable from Trash |
| PIM | Active | Native NixOS Evolution 3.60.2 plus Microsoft 365 integration is live beside Thunderbird; account and daily-use gates await credentials |
| Transcription | Pending | Requires a real Fossify recording-transfer pilot before implementation moves from Zenith to Orion |
| Conditional retirement and completion | Active | OpenVPN 3, Zed, Helix, Foot, global Node.js, and global Bun are removed declaratively; other removals remain gated separately |

## Repository checkpoints

| Repository | Branch | Commit | Purpose |
| --- | --- | --- | --- |
| NixOS configuration | `chore/workflow-system` | `41bc61b` | Discovery, paths, Git identity, and Codex defaults |
| NixOS configuration | `chore/workflow-system` | `69552b7` | Simplify flake inputs and declare workstation lifecycle tools |
| NixOS configuration | `chore/workflow-system` | `0c121a6` | Declare Garden tooling and the local workbench |
| NixOS configuration | `chore/workflow-system` | `2fb6061` | Package Garden completion declaratively |
| NixOS configuration | `chore/workflow-system` | `ad01b9b` | Enable NetworkManager's native OpenVPN plugin |
| NixOS configuration | `chore/workflow-system` | `c9ee688` | Advance VPN, desktop, agent, note, and PIM pilots |
| NixOS configuration | `chore/workflow-system` | `cfa5d6d` | Correct PWA ownership and Evolution service activation |
| NixOS configuration | `chore/workflow-system` | `c2f48df` | Restore terminal-backed Walker actions |
| NixOS configuration | `chore/workflow-system` | `6631889` | Open Walker projects at their repository root |
| NixOS configuration | `chore/workflow-system` | `ca65328` | Remove the unsafe Elephant restart trigger |
| `yookr-dashboard-new` | `feat/gogv2` | `934605d` | Remove obsolete dashboard converter |
| `rules-service` | `chore/workflow-contract` | `555d9cd` | Establish the first common repository contract |
| `yookr-api` | `chore/workflow-contract` | `a76b2b7` | Establish the HTTP and OpenAPI contract |
| `traceability-data-model` | `chore/workflow-contract` | `33cb7ff` | Establish the database and schema contract |
| `yookr-workbench` | `main` | `badc61c` | Create the workbench and isolate its Garden session |

## Deferred or externally blocked actions

None of these block work on independent pilots. Surface the exact applicable
step to the user only when it blocks the current task.

- In a separate terminal, enter this repository and run `herdr`, start `codex`,
  and ask it to read `docs/plans/workflow-system.md` without editing and report
  the exact next implementation step. Confirm Herdr shows the agent's working
  and waiting/done states, detach with `Ctrl+B` then `q`, reattach with `herdr`,
  and confirm the pane survived with its output intact.
- Run the bounded Pinta trial using a recent real edit: clipboard/open,
  selection, crop/resize/canvas, text/drawing/shapes, layers/transparency,
  basic adjustments, and PNG/JPEG export. Tell the agent whether it fully
  replaces GIMP; one of the two will then be removed.
- Install Outlook from its signed-in page as a Vivaldi web app, then tell the
  agent so its generated desktop entry can be identified and replaced by a
  stable Home Manager owner.
- During a docked Zenith session, tell the agent the external display is
  attached so its stable identity and the two-output `Super+A` pilot can be
  completed. The current session exposes only `eDP-1`.
- After activation, launch Evolution and add accounts without removing any
  existing client or changing authority: personal and old-personal through
  their existing IMAP/SMTP service, university and work through the
  `Microsoft 365` account type, and Radicale through native CalDAV, CardDAV,
  and VTODO. Complete tenant consent/sign-in when prompted, then tell the agent
  which accounts connected; the full mail/calendar/contact/task gate remains
  a daily-use pilot rather than a one-time setup claim.

- Rotate the exposed Context7 key and provide `CONTEXT7_API_KEY` through a
  mode-0600 machine-local environment file on each workstation before removing
  the static user-config header.
- Relocate the mode-0644 `/home/kiri/work/SECRETS` file to an approved private
  owner and restrict it; its contents have not been inspected.
- Move the ignored `rules-service/.env` to
  `~/.config/yookr/rules-service.env` with mode 0600; its contents have not been
  inspected or copied.
- Restore access to the locked `yookrdev/constant-store` commit or replace that
  retired dependency deliberately, then rerun `just check` in `yookr-api`.
- Deploy a GET image that exposes `/full-api-docs/openapi.json`, then rerun
  `just openapi-refresh test`; the current test deployment returns 404.
- Populate the ignored API HTTP credentials and perform the planned login plus
  harmless administrator read; no credential-bearing request has been made.
- The next Zenith switch also activates the follow-up Garden shell fix. The
  Nix-owned `gardenctl`, `gardenlogin`, and `kubectl-gardenlogin` are verified
  under `~/.nix-profile/bin`; afterward remove the duplicate mutable binaries
  `~/.garden/gardenctl` and `~/.local/bin/{gardenctl,gardenlogin,kubectl-gardenlogin}`.
- Destructive cleanup, credentials, activation, and empirical pilot decisions
  will be surfaced here before use.

## Deferred Polaris replication

Do not access or test Polaris during this implementation. Treat a Zenith pass
as representative, but retain these machine-local steps for later execution on
Polaris:

1. Activate this NixOS configuration so `networkmanager-openvpn` is installed.
2. Run `chmod 600 ~/sync/yookr-vpn.ovpn`.
3. Run `nmcli connection import type openvpn file ~/sync/yookr-vpn.ovpn`.
4. Rename the imported `yookr-vpn` connection to `Yookr VPN`, disable
   autoconnect, and add the required legacy cipher:
   `nmcli connection modify yookr-vpn connection.id "Yookr VPN" connection.autoconnect no +vpn.data data-ciphers=AES-256-CBC`.
5. Connect with `nmcli connection up "Yookr VPN"`.

## Decisions and discoveries

- Use `/home/kiri/work/repos/yookr-dashboard-new` as the reconciliation base;
  its `feat/gogv2` head is 17 commits newer than the sync copy and matches its
  remote-tracking branch.
- The user confirmed the legacy BSON migration is no longer needed and the
  former work copy is authoritative. The sync copy was explicitly deleted;
  its removal may propagate through Syncthing.
- Active repositories now live under `/home/kiri/dev/work`; inactive material
  is preserved intact under `.archive`, and the registered dashboard sensor
  worktree is under `.worktrees`.
- Removed the obsolete dashboard converter app and Python dependency. The
  dashboard flake evaluates, while the pre-existing feature work remains
  uncommitted and unstaged.
- Pruned the absent `feat/echarts-domain` worktree metadata; its branch and
  commit remain. The registered sensor worktree is valid at its new path.
- Shared Codex defaults and MCP endpoints are generated at
  `/etc/codex/config.toml`; Context7 reads its header from the environment. The
  unused generic `~/.config/mcp/mcp.json` owner is removed on next activation.
- Removed redundant legacy-path trust entries from the current Codex config;
  the existing trusted home scope covers the moved repositories.
- Bruno's transitional OpenAPI reference now follows the archived management
  repository until the HTTP pilot retires or retains Bruno.
- Post-move repository IDs, remotes, dirty counts, and the registered sensor
  worktree match the pre-move inventory. The Nix flake still evaluates.
- No-link system builds for Zenith, Polaris, and Orion pass with the migrated
  paths and declarative Codex defaults.
- Removed the unused stable Nixpkgs input and made Noctalia follow the root
  package-set pin. Added `just` to the workstation tools and selected the
  store-backed `podman-compose` provider through native `containers.conf`.
- The resulting flake check and no-link builds for all three hosts pass.
- `rules-service` now has a non-mutating direnv shell, minimal Nix toolchain and
  formatting check, native Cargo recipes, factual repository instructions,
  one `.http` request collection, explicit test/live deployment paths, and a
  corrected test-oriented environment example. The full locked Cargo check
  passes; Clippy reports 18 pre-existing advisory warnings.
- Private Cargo Git dependencies remain in the ordinary developer SSH
  boundary. They are not vendored or bridged into sandboxed Nix builds.
- `yookr-api` now owns its reviewed OpenAPI 3.1 contract, local/test/live HTTP
  metadata, curated login/health/admin-read requests, a non-mutating shell, and
  one explicit snapshot-and-diff recipe. `oasdiff` 1.31.0 is pinned with source
  and vendor hashes because Nixpkgs does not provide it.
- The API flake evaluation and built OpenAPI validation pass. Cargo stops before
  compilation because its locked `constant-store` repository is unavailable
  through both anonymous HTTPS and the working SSH identity. The test service
  is reachable, but its currently deployed GET image returns 404 for the full
  OpenAPI route already present in local source and ingress configuration.
- `traceability-data-model` preserves the existing domain/schema redesign while
  replacing automatic schema recreation with explicit `just reset`. Ordinary
  `just dev` retains its Compose volumes, and the flake check loads fixtures in
  text-ID mode plus a fresh schema in UUID-ID mode. Both the built check and the
  pinned `podman-compose` configuration validation pass.
- Gardenctl 2.14.0 and Gardenlogin 0.10.0 are pinned from their official release
  assets; the hashes match the existing binaries byte-for-byte. All three host
  builds pass, the OIDC kubectl plugin is declarative, and Zsh consumes the
  native `gardenctl rc zsh` output with its completion packaged declaratively.
- The local-only `yookr-workbench` has no remote and initially owns only
  `just k8s test`. Each invocation creates an isolated Garden session, rejects
  every environment except test, and opens K9s read-only. Its flake check and
  command catalog pass, and the live rejection path exits before Garden access.
- The user activated and rebooted into the Garden tooling, then confirmed that
  `just k8s test` opens the test shoot in read-only K9s. The initial shell error
  came from Garden writing completion into an absent Flatpak `$fpath` entry; the
  initial target warning came from the fresh session inheriting its parent's
  `KUBECONFIG`. Completion is now store-owned, and the child recipe initializes
  Garden's session-local `KUBECONFIG` before targeting instead of unsetting it.
- NetworkManager's native OpenVPN plugin is declared on Zenith and Polaris;
  no profile is embedded in Nix or imported automatically.
- Zenith's initial NetworkManager activation never established a tunnel:
  OpenVPN 2.6 preserved the profile's legacy `cipher=AES-256-CBC` setting but
  excluded it from cipher negotiation. Adding `data-ciphers=AES-256-CBC` to
  the imported connection fixes the negotiation; NetworkManager then installs
  the pushed tunnel address, default route, private routes, and DNS servers.
  Company database access, disconnect/reconnect, suspend, and reboot pass on
  Zenith, so OpenVPN 3 is retired.
- For the entire workflow implementation, do not access or test Polaris.
  Zenith results are accepted for both workstations; preserve exact deferred
  Polaris replication steps instead.
- OpenVPN 3 is removed from the configuration. A full Zenith system build
  passes, and the first password-authorized switch removed it from the live
  generation. NetworkManager reconnected the VPN successfully afterward.
- Walker's native cached Lua menu scans the four identity roots and refreshes
  when their top level changes. Its default action pipes the selected path to
  one Nix-owned `open-project` command. Elephant supplies that path without a
  terminating newline, so the launcher now accepts a successful partial read
  instead of exiting under `errexit`. It opens Neovim through the configured
  `xdg-terminal-exec` owner and leaves an interactive shell after Neovim exits.
  Elephant reads menu actions only at startup, so rare declarative menu changes
  take effect at the next login. The generated Walker configuration extends,
  rather than copies or replaces, the pinned default provider list and prefixes.
- The shared terminal-launch failure came from the Kitty package rewrite:
  unanchored `sed` changed both `Exec=kitty` and `TryExec=kitty` to include
  `-1`. Arguments are invalid in `TryExec`, causing `xdg-terminal-exec` to
  reject the configured terminal. The rewrite now changes only `Exec`; live
  resolver output selects `kitty.desktop` and retains `kitty -1`, and Yazi
  launches successfully from Walker.
- Restarting the pre-change Elephant and Walker processes loaded the corrected
  project action. The user confirmed that repository launch works and exiting
  Neovim leaves a usable shell in that repository. Passing the project root to
  Neovim now opens the configured Oil default directory explorer immediately.
- A custom restart trigger for Elephant proved unsafe: Walker requires Elephant,
  so activation stopped Walker with its backend but restarted only Elephant.
  The trigger is removed; relogging is the deliberately simple refresh path
  unless real usage proves that inconvenient. The user activated the removal,
  relogged, and confirmed both Walker and the project-root Oil action work.
- Removed the decided Niri arrow/Page Up/Down/numbered duplicates, direct quit
  and monitor-power bindings, extra screenshot modes, first/last and centering
  actions, repeated resize families, and their four shortcut-only scripts. The
  existing `Super+A` helper remains until a two-output session can validate its
  bounded name-based replacement.
- Home Manager now owns the existing Vivaldi launcher filenames for Actual and
  WhatsApp at the higher-precedence user-data location, so both invoke Vivaldi
  8.1.4087.70 with the `Default` profile and stable app ID. Direct activation
  replaced both generated files with managed links and retained the originals
  as adjacent `.bak` files. The entries use native forced ownership because
  Vivaldi may regenerate those exact paths. Outlook is not installed yet, so no
  ID was guessed.
- The first `nixos-maintainer` skill is instruction-only, Nix-owned, and passes
  the skill-creator validator. It encodes repository-specific ownership,
  research, formatting, no-switch, and affected-host validation behavior
  without duplicating generic agent guidance or adding scripts.
- Removed Zed, the inactive Helix modules and note integration, Helix's cache
  settings and complete lock subgraph, and inactive Foot modules. Neovim and
  Kitty remain the sole declared editor and terminal. A repository-wide search
  found no configured npm caller, so global Node.js and Bun are also removed;
  project shells retain language runtimes where needed.
- Pinta is added beside GIMP only for its bounded trial; neither outcome is
  preselected before real editing evidence.
- `sync/notes` is now the sole declarative notebook owner, with `daily`,
  `meetings`, and `transcripts` directories, a native `zk daily` alias, and a
  `Super+N` dedicated Kitty/Neovim launcher. The five unique authored work notes
  were copied byte-for-byte, and both distinct todo lists were merged without
  dropping an item. Syncthing returned to idle with no needed files, pull
  errors, or new conflicts. The user confirmed the daily launcher and migrated
  contents, then explicitly approved moving the intact `sync/work/notes`
  rollback copy to desktop Trash. The pre-merge todo copies in `/tmp` may now
  expire normally.
- Evolution 3.60.2 is composed through Nixpkgs with `evolution-ews` 3.60.2,
  whose pinned source contains the separate native Microsoft 365 mail,
  calendar, contacts, recurrence, and OAuth backends. Live inspection caught
  that overriding `evolutionWithPlugins.plugins` replaced its default Evolution
  package, and that a Home Manager package alone did not register the data
  server on D-Bus. The pilot now uses NixOS's native `programs.evolution`
  integration with the EWS plugin beside Thunderbird. The follow-up activation
  succeeded, its source-registry service activates through D-Bus, no account is
  preconfigured, and no authority is changed.
- Named database connections and a Marimo-to-HTML report remain workbench
  evaluation evidence, not scaffolding requirements. Add them only for a real
  cross-system investigation that gives the queries and report durable value.
- Run independent pilots in parallel, but gate every retirement separately.