Workflow system execution

Source: ../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.

Execution discipline

Advance every safe independent lane before asking the user to act. Batch declarative changes behind one user-controlled activation and consolidate empirical, credential, hardware, and approval gates into one checklist only after no autonomous work remains. A single pilot reaching its user gate does not make it the global next step while another pilot can still progress.

Current checkpoint

Tranche: autonomous consolidation across repositories, tools, and pilots
State: autonomous implementation exhausted; consolidated gates await the user
Branch: chore/workflow-system
Baseline: nix flake check --no-build --quiet and a no-link Zenith system build passed on 2026-09-05 after the consolidated workstation retirement and rclone preparation; 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. Four fresh local clones pass their flake checks, expose their tracked command catalogs, and remain clean after shell entry. The dashboard contract additionally passes its full check and a bounded two-process development smoke test. The dashboard and traceability PostgreSQL stacks also ran concurrently while both repositories' checks passed; all test processes and containers were then stopped.
Next: present one consolidated user batch covering the built activation and the independent empirical, credential, hardware, and approval gates below.

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	Four clean-checkout contracts and read-only Kubernetes pass; data-science overlaps uncommitted work, while API, database, report, and secret inputs remain externally gated
Desktop navigation and interaction	Active	Walker project and terminal actions plus stable Actual/WhatsApp launchers work; Outlook and two-output checks remain
Agent workflow	Waiting for user	The `nixos-maintainer` skill validates and matches its live owner; external policy blocks nested Codex evaluation without approval, and Herdr awaits its first 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	Superseded HTTP/database/note tools are removed with earlier retirements; Bruno, DBeaver, image editors, and PIM clients remain behind separate gates

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
NixOS configuration	`chore/workflow-system`	`d085512`	Advance from Walker to the agent pilot
NixOS configuration	`chore/workflow-system`	`ee64a7b`	Retire superseded tools and prepare the S3 pilot
`yookr-dashboard-new`	`feat/gogv2`	`934605d`	Remove obsolete dashboard converter
`yookr-dashboard-new`	`feat/gogv2`	`8e6e4bc`	Establish its project contract and native lifecycle
`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
`traceability-data-model`	`chore/workflow-contract`	`774e710`	Remove Mathesar and simplify the local stack to PostgreSQL
`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.

Activate the consolidated Zenith build with cd ~/.config/nixos && nh os switch. This removes the retired tools and installs rclone; only the user may run it.
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.
On Android, complete the DAVx5/Radicale and Tasks.org pilots described in the discovery plan, including correct default accounts, recurrence, reminders, and Microsoft To Do within its documented limits.
Make one Fossify recording on the Pixel and let Syncthing transfer it. Do not rename or move it manually; the agent must first observe the real write and settlement behavior before implementing Orion automation.
Reauthenticate the GitHub CLI with gh auth login -h github.com; its current kirigar token is invalid. The agent can then complete the read-only PR and isolated review-worktree gate without more direction.
Explicitly authorize the five ephemeral, read-only codex exec skill-scope checks if sending this private repository to another authenticated Codex session is acceptable. External policy correctly rejected them without that approval; static skill validation already passes.
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.
Move the ignored yookr-dashboard-new/.env to its approved machine-local mode-0600 owner, then update .envrc; the non-secret repository contract is already complete.
Commit or otherwise hand off the extensive dirty yookr-data-science work before its flake, live-fetch defaults, local credentials, and missing project contract are changed. Those files overlap the active work directly.
Explicitly approve moving the stale ~/.config/codex tree to Trash if its old authentication, conversations, databases, and plugins are no longer needed.
Explicitly approve removing the orphaned Podman volume traceability-data-model_mathesar-secrets and the old mathesar_django database if no Mathesar rollback is wanted. They are disconnected from the repository but preserved because deletion would be irreversible.
Supply one real Yookr S3 task plus a least-privileged remote and authorize one bounded upload. rclone is prepared, but no remote or wrapper is guessed.
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.

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:

Activate this NixOS configuration so networkmanager-openvpn is installed.
Run chmod 600 ~/sync/yookr-vpn.ovpn.
Run nmcli connection import type openvpn file ~/sync/yookr-vpn.ovpn.
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.
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 is absent.
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.
The verified-empty legacy directories ~/work/.data/mongodb, ~/work/.data, and ~/work/repos are removed. The stale ~/.config/codex tree is preserved because it contains old authentication and conversation state; moving that recoverably requires explicit user approval.
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.
Mathesar is removed from traceability-data-model; the development stack now owns only PostgreSQL plus the explicit schema-reset job. The existing named volume and its historical local role are preserved to avoid stranding data. just reset, just dev, the PostGIS fixture query, Compose validation, and the flake check pass after the simplification.
yookr-dashboard-new now has the same minimal project contract: a non-mutating flake shell, just dev over its existing Process Compose graph, just check, factual AGENTS.md and README guidance, a flake formatter and formatting check, and a complete public environment example. Its full type, lint, and format checks pass; a bounded smoke test reached ready MongoDB and Vite processes and stopped cleanly. The commit contains only contract files; the user's existing dashboard source work remains unstaged and untouched.
Fresh local clones of rules-service, yookr-api, traceability-data-model, and yookr-dashboard-new all pass nix flake check, expose their tracked just catalogs, and remain clean after entering their development shells. Credential-bearing and externally blocked checks remain separate gates.
yookr-data-science still lacks a committed project contract, its untracked flake mutates the checkout during shell entry, and its explicit fetch pipeline still targets live services. Those exact files overlap extensive uncommitted user work, so a partial agent edit would be unsafe and misleading; wait for a commit or deliberate handoff before changing them coherently.
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. The former mutable Garden binaries and generic MCP output are already absent, so their stale cleanup gate is closed without further user work.
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.
Postman, HTTPie, Posting, and Resterm are removed after their valuable request definitions moved to tracked HTTP owners; Bruno remains through its own pilot. Rainfrog, dblab, Harlequin and its profile, Tabularis, DbGate, pgAdmin, MongoDB Compass, pgModeler, tbls, global usql, and global MariaDB are removed; Dadbod and wrapper-local clients remain, while DBeaver stays through its gate. Obsidian, Planify, and Calcure are removed after note and task authority was established. Pinta/GIMP and the Evolution-era PIM clients remain independently gated.
rclone is installed as the only preparation for the selected S3 pilot. No remote, wrapper, or interactive browser is added before a real task and least-privileged credentials exist.
GitHub PR review is blocked by the invalid kirigar CLI token, not repository state. The agent can complete the read-only review and isolated worktree gate autonomously after reauthentication.
The live nixos-maintainer skill matches its Nix source and passes static validation. Five ephemeral read-only behavioral checks were deliberately not run because external policy requires explicit approval before another authenticated Codex session receives this private repository.
In zsh, never use lowercase path as a loop or local variable: it is tied to PATH. A diagnostic command temporarily hid normal executables by doing so; the declarative session environment was correct and needed no patch.
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.

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