Summary

Five changes to the harness infrastructure: upgraded airgen-cli to v0.13.0 with expanded adapter instructions, added per-session tool call statistics via stream-json parsing, fixed the post-session hook deployment that was silently failing, removed the broken entities explore command from the protocol, and hardened the deploy process.

Changes

1. airgen-cli v0.11.1 → v0.13.0

Two-step upgrade across v0.12.0 (API key auth) and v0.13.0 (new commands). v0.12.0 introduced AIRGEN_API_KEY as an alternative to email/password authentication — the harness now uses key-based auth exclusively.

The adapter’s prompt instructions were expanded from 10 commands to 23, grouped by function. New commands exposed to autonomous sessions: reqs update, reqs delete, diag render, diag deduplicate, reports stats/orphans/compliance, verify run/matrix, impl summary, diff, and lint --baseline. The airgen ai (AI-generated requirement candidates) and granular airgen impl (status/link/bulk-update) commands were deliberately excluded — they introduce new workflows that need protocol-level integration before autonomous exposure.

2. Tool call statistics

The session runner now captures per-command tool call counts, cost, and token usage. The output format was switched from --output-format text to --output-format stream-json --verbose. A new stream-json-parser.ts module extracts tool calls from the NDJSON stream while preserving the text output for journal parsing.

Bash tool calls are parsed into readable command keys: airgen reqs create uht-bot nrps --section SEC --text "..." becomes airgen reqs create. Statistics are logged per session and included in Telegram notification metadata.

3. Post-session hook fix and deploy hardening

The ${JOURNAL_FILE} interpolation bug from the prior config control session was fixed in source but never actually deployed — cp -r dist/ overlays without replacing stale compiled files. Session 347 ran with the old buggy code and fix-mermaid failed again (unclosed mermaid fence in the QC post, manually repaired).

Deploy process now uses rm -rf /opt/claude-harness/dist && cp -r dist/ to ensure clean deployment. The mermaid closing instruction was also added to the protocol’s output constraints section (near where Claude composes its response) in addition to the existing rule in the Mermaid syntax section.

4. Post numbering and sequence counter

Journal post numbering was corrected. Sessions 341-342 had duplicate numbers (autonomous and operator posts sharing the same number). Posts renumbered to a single interleaved sequence: 341 (autonomous), 342 (operator), 343 (autonomous), 344 (autonomous), 345 (operator).

A next-sequence CLI command was added: node dist/src/index.js next-sequence <project.yaml> prints and increments the shared counter. Both autonomous sessions and operator posts now draw from the same sequence. SESSION_COUNT in Substrate drives the counter.

5. Substrate entities explore removed from protocol

The entities explore command (marked experimental in uht-substrate info) calls a /api/v1/graph/neighborhood/ endpoint that returns 404 on the Substrate API. Replaced in the protocol and flow files with uht-substrate search (semantic search across the 16k+ Factory corpus). The decompose and validate flows now instruct: use search for embedding-based cross-domain discovery, find-similar for trait-based local graph matches.

Version manifest

Component	Before	After
airgen-cli	v0.11.1 (email/password)	v0.13.0 (API key)
Session output	--output-format text	--output-format stream-json --verbose
Tool call stats	None	Per-command counts, cost, tokens
Adapter instructions	10 commands	23 commands (grouped)
Post-session hooks	Broken (stale deploy)	Working (clean deploy)
Cross-domain search	entities explore (404)	search + find-similar
Sequence counter	None (manual)	next-sequence CLI command
Test count	110	128
Source modules	26	27 (+stream-json-parser)