clarion-setup

name	clarion-setup
description	Bootstraps the Clarion Intelligence System on Zo Computer. Run this once after installing — clones the source repo, installs the ai_buffett_zo Python library, creates the workspace data tree under /home/workspace/clarion/ (auto-detected on Zo), auto-installs all nine sibling clarion-* skills (regime-check, sec-research, single-stock-eval, expected-return-calc, value-screener, thesis-write, thesis-monitor, watchlist-update, living-letter-update) under /home/workspace/Skills/, and registers the sec-indexer background service. Idempotent (safe to re-run). The only manual step is one batched human checkpoint near the end (SEC EDGAR name + email, and creating the ZO_API_KEY secret). Persona routing for Clarion is opt-in via a separate prompt after install ("install Clarion personas and routing rules"). Use when the user asks to "set up Clarion" or "install Clarion".
metadata	{"author":"cis.zo.computer","category":"External","display-name":"Clarion Setup","homepage":"https://github.com/jingerzz/clarion-intelligence-system"}

Clarion Setup

Bootstraps the Clarion Intelligence System on a Zo workspace. Run this once before any other clarion-* skill.

Flow at a glance

This skill is designed for a single-prompt install experience that delivers the working system (library, skills, service) fast — typically ~30 seconds of autonomous work plus the user's time creating the ZO_API_KEY secret. Steps 1–3 run autonomously (clone, library, data tree, register service). Step 4 is one batched human checkpoint — the user supplies their SEC EDGAR identification and creates the ZO_API_KEY secret in Zo Settings. Steps 5–7 resume autonomously to apply the user's input, restart the service, verify it's running, and report.

Personas and routing rules are NOT installed by this skill. They're the chat-layer discipline (regime-first framing, kill-condition enforcement, persona handoff between Macro Sentinel → Analyst → Thesis Architect → Portfolio Manager). The bare install delivers everything needed to evaluate a stock from chat; persona routing is opt-in via a follow-up prompt described in Step 7 — typically a separate ~3-minute step the user takes after they've tried a few queries.

Walk through the steps below in order. Stop and surface any failure to the user immediately — do not proceed past a failure.

Step 1 — Clone or update the source repo

The repo holds the Python library, the sec-indexer service code, and templates.

If /home/workspace/clarion-intelligence-system does NOT exist:

gh repo clone jingerzz/clarion-intelligence-system /home/workspace/clarion-intelligence-system

If it exists, update it:

git -C /home/workspace/clarion-intelligence-system pull --ff-only

Step 2 — Run the setup script

python /home/workspace/clarion-intelligence-system/skills/clarion-setup/scripts/setup.py

The script is idempotent. It will:

• Install the ai_buffett_zo library editable (auto-detects whether to use --system)
• Create the ~/clarion/{data/equities,sec,queue,theses,watchlists,letters}/ data tree
• Write a default ~/clarion/config.json if missing (preserves any existing config — including any sec_user_agent you already customized)
• Verify the sec-indexer console script is on PATH
• Install every sibling clarion-* skill from the repo into /home/workspace/Skills/ (refreshes any already-installed copies; pass --skip-skills to opt out)
• Print service registration parameters between --- BEGIN SERVICE_REGISTRATION --- and --- END SERVICE_REGISTRATION ---
• Print a USER_ACTION_REQUIRED block (you'll surface this in Step 4)
• Print a final SETUP_RESULT: ok line on success, or SETUP_RESULT: error: <reason> on failure

If you do NOT see SETUP_RESULT: ok, surface the error to the user verbatim and stop.

Step 3 — Register the sec-indexer service

Use the register_user_service agent tool with the parameters printed in the SERVICE_REGISTRATION envelope:

• label: sec-indexer
• mode: process
• entrypoint: sec-indexer
• workdir: /home/workspace
• env_vars: pass as a JSON object — see env_vars formatting below
• description: Clarion sec-indexer — background SEC EDGAR filing indexer

env_vars formatting (critical — common failure mode). env_vars is an object-valued parameter, not a stringified JSON. Pass it exactly as printed in the SERVICE_REGISTRATION envelope:

{"ZO_API_KEY": "$ZO_API_KEY", "CLARION_DATA_ROOT": "/home/workspace/clarion"}

Do not wrap it in quotes and escape it like "{\"ZO_API_KEY\": \"$ZO_API_KEY\", ...}". If the tool call appears to require escape sequences inside env_vars, stop and re-form the call — the parameter is an object, not a string. Models that try to escape this end up generating malformed input that either fails outright or — worse — succeeds with corrupted values (env vars inlined into the entrypoint shell-string, trailing XML-tag artifacts appended to the entrypoint, CLARION_DATA_ROOT silently dropped). The verification at Step 6 catches the corrupted-success case; the prevention is to get the env_vars shape right here.

Expected state after Step 3: the service is in FATAL or BACKOFF. This is normal and expected. $ZO_API_KEY resolves from a Zo secret that doesn't exist yet (the user creates it in Step 4). The supervisor will try to launch sec-indexer, the binary will fail to authenticate against Zo's API, and the service will retry-backoff. Do NOT call service_doctor yet. Do NOT delete and re-register. Continue to Step 4. The restart in Step 5, after the secret exists, brings the service to RUNNING.

If register_user_service itself returns an error (not just a FATAL state — an actual tool error), check the env_vars formatting above first, then surface the error.

Step 4 — Batched human checkpoint (the only manual step)

Pre-check (skip the whole checkpoint on a clean re-run). Before asking the user for anything, check both of:

1. /home/workspace/clarion/config.json's sec_user_agent field — is it the placeholder Clarion Intelligence System ([e-mail]), or a real user value?
2. service_doctor(service="sec-indexer") — is the service already RUNNING with non-zero uptime? (If yes, the ZO_API_KEY secret already exists, since the service couldn't have started without it.)

If sec_user_agent is a real value AND the service is already RUNNING, skip Step 4 entirely — there's nothing for the user to do. Tell the user "detected a complete prior install — skipping the human checkpoint and going straight to a refresh restart." Jump to Step 5b (restart only, no config.json write needed).

Otherwise, you need at least one of two inputs from the user. Surface both together so they can multitask — the user can type their SEC identification in chat while simultaneously navigating Zo Settings to create the secret.

Input A — SEC EDGAR identification

First, check /home/workspace/clarion/config.json — read the sec_user_agent field. If it is the placeholder Clarion Intelligence System ([e-mail]), you need a real value from the user. Ask:

SEC EDGAR requires Clarion to identify itself in every API request. Type your name and email in the format: Jane Doe [e-mail]. This will be sent in the User-Agent header of every SEC request from your machine — only you and the SEC see it. SEC's fair-access policy asks every API consumer to identify themselves.

Reply with that one line. While you're doing that, also start Input B below.

If sec_user_agent is already a non-placeholder value (a previous install set it), skip Input A and use what's already in config.json.

Input B — Create the ZO_API_KEY secret in Zo Settings

The setup script's stdout includes a block bounded by --- BEGIN USER_ACTION_REQUIRED --- and --- END USER_ACTION_REQUIRED ---. Paste the contents of that block (everything between the two sentinels) into chat verbatim, below your Input A request. Do not summarize, paraphrase, or condense — the block is dummy-proofed for non-technical users with exact menu paths and the exact secret name (ZO_API_KEY, uppercase, with underscore — the most error-prone part).

Wait for the user to reply with:

• A line in the format Name [e-mail] (for Input A) — unless you already had a non-placeholder sec_user_agent, in which case there's nothing to wait for here.
• The word done (or any clear confirmation) that they've created the ZO_API_KEY secret (for Input B).

If the user only replies to one of the two, prompt for the other before continuing.

Step 5 — Apply user inputs and restart the service

5a — Write the SEC user-agent to config.json (only if Input A produced a value)

Substitute the user's reply into this command and run it:

python3 -c "import json, pathlib; p = pathlib.Path('/home/workspace/clarion/config.json'); d = json.loads(p.read_text()); d['sec_user_agent'] = '<USER_INPUT_VERBATIM>'; p.write_text(json.dumps(d, indent=2))"

Replace <USER_INPUT_VERBATIM> with the user's exact reply (no quotes around it inside the Python string — the outer quotes are already there). Confirm the write by reading the file back and showing the sec_user_agent line.

5b — Restart the sec-indexer service

Call update_user_service with the existing sec-indexer service_id and action="restart". This:

• Causes the supervisor to re-evaluate $ZO_API_KEY (now that the secret exists)
• Restarts the sec-indexer process (which re-reads config.json on startup, picking up the new sec_user_agent)

Confirm the restart command succeeded.

Step 6 — Verify the service is actually running (do not skip)

Call the service_doctor agent tool:

service_doctor(service="sec-indexer")

Expected: status is RUNNING with non-zero uptime. The tool also reports listening status, source-file freshness, and suggests fixes for any detected issues.

If the result shows FATAL, BACKOFF, EXITED, STOPPED, or any non-RUNNING state, the registration is genuinely broken. The two failure modes you'll see in practice:

1. Trailing characters in the entrypoint. Check the registered service's entrypoint field via list_user_services(). It must be exactly sec-indexer. If it's something like sec-indexer</, sec-indexer\n, or has env vars inlined into the entrypoint shell-string, the model output got corrupted during the Step 3 tool call.
2. Missing or malformed env_vars. If ZO_API_KEY or CLARION_DATA_ROOT aren't in the registered service's env_vars as separate keys, the binary will fail to authenticate or write to the wrong data root.

Inspect logs via shell if needed:

tail -50 /dev/shm/sec-indexer.log
tail -50 /dev/shm/sec-indexer_err.log

If anything is wrong, delete_user_service the broken one and re-do Step 3 — re-read the env_vars formatting guidance carefully. Do not tell the user setup is complete until service_doctor(service="sec-indexer") reports RUNNING with non-zero uptime.

Verify the service is running CURRENT code (issue #55)

service_doctor confirms the process is RUNNING, but a process can be RUNNING on stale code — an editable reinstall (uv pip install -e) does NOT reload an already-running service. On a re-run that pulled new code, a service that wasn't restarted will keep executing the old code, and re-indexing will silently produce wrong data. Confirm freshness:

clarion-sec-research doctor

Expect Indexer: up to date (commit …). If it reports Indexer: STALE — running commit X but installed code is Y, the service is still on pre-update code: restart it (repeat Step 5b) and re-run clarion-sec-research doctor until it reports up to date. Do not report setup complete while doctor reports STALE. (If it reports "no runtime marker", the service hasn't started since this version was installed — restart it.)

As a separate (weaker) sanity check that the binary is reachable on PATH:

sec-indexer --help

This proves the executable resolves on PATH, but does NOT prove the service is running. Step 6's service_doctor is the actual validation.

Step 7 — Report and explain

Tell the user:

Clarion is set up.

• Source: /home/workspace/clarion-intelligence-system/
• Workspace data: the path printed in the [2/6] Creating data tree under … line from setup.py (typically /home/workspace/clarion/ on Zo, ~/clarion/ on a local machine — auto-detected)
• Background service: sec-indexer (running)
• Skills installed under /home/workspace/Skills/: every sibling clarion-* skill from setup.py's [5/6] block. List the actual names returned.
• SEC EDGAR identification: <the user's name and email from config.json> (the actual value, not the placeholder).

Try it out — ask me things like "evaluate AAPL", "what's the market regime?", "index NVDA's latest 10-K", or "run a value screen on AAPL, KO, JNJ". The skills work as standalone CLIs too.

Optional next step — install Clarion's persona routing for the full chat experience. This adds the 7 Clarion personas (Macro Sentinel, Analyst, Thesis Architect, Portfolio Manager, etc.) and 8 routing rules that enforce regime-first framing, kill-condition discipline, and automatic persona handoff. Takes ~3 minutes. To opt in, just say: "install Clarion personas and routing rules". To skip: do nothing — the skills above all work without it.

If anything in this report differs from the expected state (e.g., service not RUNNING, sec_user_agent is still the placeholder), call this out explicitly. Do not paper over partial-install state.

Idempotency

Re-running this skill is safe. Each step:

• Repo clone: skipped if already cloned (just git pull --ff-only)
• Library install: re-runs uv pip install -e (no harm)
• Data tree: mkdir -p (no harm)
• Config.json: preserved if present — including any sec_user_agent the user previously set. The setup script does NOT overwrite an existing config.
• Skill install: each sibling clarion-* skill in /home/workspace/Skills/ is refreshed (overwritten) with the upstream copy. This is the intended path to pull in upstream skill fixes after a git pull.
• Service registration: if the user already has a sec-indexer service, register_user_service should report it exists; treat that as success and continue.
• Human checkpoint: Step 4's Input A is skipped if config.json already has a non-placeholder sec_user_agent. Step 4's Input B is essentially "if the secret already exists, the user replies done immediately and the SKILL.md's USER_ACTION_REQUIRED message instructs them this is OK."

Personas and routing rules are not touched by re-runs because they're not installed by this skill. They live in Zo Settings → AI → Personas / Rules and are managed by the user (or by the separate persona-install prompt). A re-run of clarion-setup never adds, removes, or modifies personas or rules.

Re-running to pick up source updates

Editable installs (uv pip install -e) do NOT reload an already-running service — the sec-indexer process keeps the Python modules it imported at startup in memory. After a git pull brings in new code, you MUST restart the service for the changes to take effect. Skipping the restart is silent: the logs look healthy, filings get marked indexed, and the old code quietly produces wrong data (this is exactly what happened in issue #55 — an extraction fix was pulled but the service kept running pre-fix code, so re-indexed filings stayed broken).

A full setup re-run handles this: the clean-re-run path jumps to Step 5b (restart unconditionally), and Step 6's clarion-sec-research doctor check then confirms the running code matches what's installed. Always let the restart happen on a re-run — do not skip Step 5b even if config is unchanged.

If code was updated outside this flow (a bare git pull without re-running setup), the service is almost certainly stale. Run clarion-sec-research doctor; if it reports STALE, restart the sec-indexer service first.

Applying extraction fixes to an already-indexed corpus (issue #57). A code update only changes how filings are parsed; it does not touch filings already on disk. After confirming the service is current (doctor → up to date), run clarion-sec-research reindex to re-extract the existing corpus. It re-extracts only filings built by older code (current ones skip), so it's safe to run after every upgrade — and necessary for extraction/parsing fixes to reach data the user indexed before the upgrade.

On error

If any step fails, do not silently proceed. Read the error, summarize the cause, and offer the user the next step to take. Common cases:

• gh: command not found — Zo should ship gh. If missing, the user's workspace is in a non-standard state; ask them to contact Zo support.
• uv: command not found — same.
• uv pip install fails with venv error — the script tries --system automatically; if it still fails, ask the user to share the full error.
• register_user_service fails with a JSON-escaping or "runner stopped" error — re-read the env_vars formatting guidance in Step 3. The most common cause is env_vars being passed as a stringified JSON instead of an object. Re-form the call and retry.
• service_doctor shows non-RUNNING after Step 5's restart — follow the Step 6 troubleshooting (inspect entrypoint via list_user_services(), inspect logs, delete + re-register if entrypoint is corrupted). Do NOT mark setup complete.