Changelog

Config (breaking) — pr-pipeline worktree setup

worktreeInstallDeps (boolean, previously defaulted to true) has been removed. Replace it with worktreeSetupCommands (array of shell strings, defaults to []). Each command runs via sh -c with cwd set to the worktree root; the token {{mainPath}} expands to the source repo path. Failures are non-fatal (logged as warnings). Migration example:
```
"worktreeSetupCommands": [
  "pnpm install --frozen-lockfile",
  "cp {{mainPath}}/docker/.env docker/.env"
]
```
The old automatic lock-file detection (pnpm-lock.yaml, package-lock.json, yarn.lock, composer.lock, go.mod) is no longer performed; add the relevant install command explicitly if your repo needs it.

Config (breaking)

The following top-level and plugin fields were removed (they were ignored by older builds or unsafe to keep in JSON):

Top level: model (use agents.<id>.defaultModel or AGENTS_*_MODEL env), adapters (use plugins / the server GET / and GET /api plugins list).
local-repos-plugin: validation.validateOnStartup (only failOnMissing is used), discovery, nested repoContext.summaryGeneration (use top-level summaryGeneration).
jira-adapter: webhookPath (path is fixed under /plugins/.../webhook/jira).

Jira credentials: do not keep apiToken / email / baseUrl in committed example files; set JIRA_API_TOKEN, JIRA_EMAIL, JIRA_BASE_URL in production. Rotate any token that was ever in a local file.

pr-pipeline: configurable agent

The PR pipeline no longer hardcodes opencode as the coding agent. Agent selection now follows a three-level precedence:

prAgent option on @agent-detective/pr-pipeline (per-plugin override).
App-level agent config field or AGENT env var (global default).
opencode (built-in fallback, unchanged behaviour when nothing is set).

New keys (defaults match previous hardcoded behavior)

agents.runner: timeoutMs, maxBufferBytes, postFinalGraceMs, forceKillDelayMs — see config/local.example.json.
Env: AGENTS_RUNNER_TIMEOUT_MS, AGENTS_RUNNER_MAX_BUFFER_BYTES, AGENTS_RUNNER_POST_FINAL_GRACE_MS, AGENTS_RUNNER_FORCE_KILL_DELAY_MS, OBSERVABILITY_REQUEST_LOGGER_EXCLUDE_PATHS (comma-separated paths).
Jira (options or env JIRA_AUTO_ANALYSIS_COOLDOWN_MS, JIRA_MISSING_LABELS_REMINDER_COOLDOWN_MS): autoAnalysisCooldownMs, missingLabelsReminderCooldownMs.
local-repos repoContext (or env REPO_CONTEXT_GIT_COMMAND_TIMEOUT_MS, REPO_CONTEXT_GIT_MAX_BUFFER_BYTES, REPO_CONTEXT_DIFF_FROM_REF): gitCommandTimeoutMs, gitMaxBufferBytes, diffFromRef.
local-repos summaryGeneration (or SUMMARY_MAX_OUTPUT_CHARS env): maxOutputChars.
Observability: observability.requestLogger.excludePaths.

Plugin option objects for bundled plugins are now validated with .strict(); unknown keys fail at plugin load with a Zod error.

API

GET / and GET /api root payload: adapters was replaced with plugins (package names from config).

See also migration.md and configuration.md.