@iowarp/clio-coder 0.4.1 → 0.4.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (437) hide show
  1. package/CHANGELOG.md +92 -0
  2. package/CONTRIBUTING.md +59 -36
  3. package/README.md +404 -472
  4. package/SECURITY.md +2 -1
  5. package/dist/{acp-ZILU3AUO.js → acp-TMDQZDIG.js} +7 -7
  6. package/dist/{agents-HYWGBGQR.js → agents-5N5NG3XG.js} +28 -28
  7. package/dist/assets/codewiki.json +1 -1
  8. package/dist/{auth-N3QT7CBO.js → auth-Z5CCBXKQ.js} +8 -9
  9. package/dist/{builtins-UJLMOVOV.js → builtins-K6TNDT24.js} +4 -4
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  92. package/dist/{chunk-7RY5VZPH.js → chunk-ZW4HH5JJ.js} +6 -6
  93. package/dist/cli/index.js +33 -32
  94. package/dist/{clio-IT3G3VQH.js → clio-7VB377CC.js} +7 -7
  95. package/dist/{code-nav-RK6S7F6E.js → code-nav-YVLCYA7V.js} +85 -17
  96. package/dist/{config-3QZRWZJF.js → config-4HVOS65E.js} +88 -43
  97. package/dist/{configure-FL7Y3KJF.js → configure-PIWO7B24.js} +10 -10
  98. package/dist/{context-5HE7ODYK.js → context-IYEHL3WQ.js} +33 -31
  99. package/dist/{context-XNHL75JV.js → context-KQYIWPWT.js} +47 -34
  100. package/dist/{context-KYQFRVDC.js → context-N6ZE3LGJ.js} +11 -11
  101. package/dist/{context-clear-N545L53A.js → context-clear-G4OGZJDS.js} +33 -31
  102. package/dist/{context-working-set-QHKXSV2F.js → context-working-set-BWLF6LJP.js} +7 -7
  103. package/dist/{dispatch-runner-RGIE5PCT.js → dispatch-runner-2QQAITS3.js} +38 -38
  104. package/dist/{docs-5NAF6AU7.js → docs-PD3EXDKU.js} +21 -20
  105. package/dist/{doctor-ZGPEGHIP.js → doctor-LHBD36VU.js} +23 -22
  106. package/dist/{eval-GXLL44RD.js → eval-C45FYRJ6.js} +21 -20
  107. package/dist/{eval-inventory-HBWSWQOK.js → eval-inventory-6DEJPLBF.js} +2 -2
  108. package/dist/{evidence-HWLBRH3Q.js → evidence-6SHONYAF.js} +30 -28
  109. package/dist/{evolve-FTZBMNVW.js → evolve-KRKMV72X.js} +30 -28
  110. package/dist/{extensions-VHRBEID7.js → extensions-KPZ2UHBB.js} +5 -3
  111. package/dist/{fleet-CKZHJWZJ.js → fleet-IVTCKDHT.js} +62 -61
  112. package/dist/{fleet-commands-EXDXBMV6.js → fleet-commands-EDWL3IT7.js} +5 -5
  113. package/dist/{fleet-decisions-OTHB6KRL.js → fleet-decisions-YP3YEFGK.js} +4 -4
  114. package/dist/{fleet-graph-YTEZUCUT.js → fleet-graph-ZFWKHY2M.js} +16 -14
  115. package/dist/{fleet-inspect-SS6YMDCK.js → fleet-inspect-FVUNCBML.js} +31 -29
  116. package/dist/{fleet-preflight-PBY4VYOM.js → fleet-preflight-UN5XED4R.js} +2 -2
  117. package/dist/{fleet-validate-KMEM5L3S.js → fleet-validate-XOWC4HSX.js} +17 -15
  118. package/dist/{fleet-verify-QD5M7E7Q.js → fleet-verify-UN3SODEL.js} +30 -28
  119. package/dist/{fleet-view-WAMJYNDT.js → fleet-view-TWHJKCN6.js} +31 -29
  120. package/dist/{init-5XQRBOFV.js → init-T2QORQ3Y.js} +50 -49
  121. package/dist/{interop-34TVO25M.js → interop-IN5I2A66.js} +5 -5
  122. package/dist/{library-3QY6KF57.js → library-LSCATDLZ.js} +15 -13
  123. package/dist/{memory-L4UTIIIW.js → memory-HYOKAGGJ.js} +31 -29
  124. package/dist/{models-ZVX3QOWE.js → models-2GPMFYCM.js} +22 -21
  125. package/dist/{monitor-CEKVSYTS.js → monitor-E4ASVUJH.js} +34 -32
  126. package/dist/{orchestrator-77BAP6BC.js → orchestrator-DDMPR3PY.js} +984 -583
  127. package/dist/{panes-7STHOAUJ.js → panes-E3RUXOW5.js} +4 -4
  128. package/dist/{panes-SHAUIRXY.js → panes-IXKLOKA2.js} +23 -8
  129. package/dist/{reset-EOLM7GVE.js → reset-OAQP3W4O.js} +4 -4
  130. package/dist/{resources-74GKTLSF.js → resources-OTRSN34L.js} +15 -13
  131. package/dist/{run-HBAUJNNZ.js → run-5DEYH5QK.js} +60 -59
  132. package/dist/{share-G3APVLVP.js → share-IHWTLO3M.js} +19 -15
  133. package/dist/{skills-35HHUKCR.js → skills-IYMXMKW4.js} +17 -15
  134. package/dist/{skills-eval-QN4HSHDC.js → skills-eval-DROHSJAR.js} +36 -36
  135. package/dist/{skills-inventory-J357J34F.js → skills-inventory-D7X4L4ZX.js} +15 -13
  136. package/dist/{slash-commands-JZZCQA32.js → slash-commands-QBM7UZ3B.js} +21 -18
  137. package/dist/{steer-XAVHJM22.js → steer-Z5DO23FJ.js} +2 -2
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  139. package/dist/{terminal-lease-JOPFUVEM.js → terminal-lease-YREJ3JX2.js} +5 -5
  140. package/dist/{tools-MKNWVPBH.js → tools-5B7RO6MV.js} +4 -4
  141. package/dist/{trace-ECQ7TIYZ.js → trace-YMGMUM6A.js} +55 -7
  142. package/dist/{upgrade-H7TOM7YL.js → upgrade-PXK3S2YM.js} +11 -9
  143. package/dist/{usage-X52N3IDJ.js → usage-ME5MPXGX.js} +36 -34
  144. package/dist/{verifiers-EJTVVSMA.js → verifiers-BVZ7IWOO.js} +5 -5
  145. package/dist/{verify-YJL6XET2.js → verify-5K7ZKQFC.js} +4 -4
  146. package/dist/{web-fetch-MPIFL3LL.js → web-fetch-MPARV2K7.js} +2 -2
  147. package/dist/{wiki-generate-4NDZTQ4B.js → wiki-generate-F5W5QTYY.js} +48 -47
  148. package/dist/{with-panes-OBOBFIIR.js → with-panes-BYOJCLAM.js} +51 -255
  149. package/dist/worker/entry.js +45 -30
  150. package/docs/README.md +176 -81
  151. package/docs/{acp.md → architecture/acp.md} +36 -20
  152. package/docs/{alcf-provider.md → architecture/alcf-provider.md} +8 -5
  153. package/docs/{architecture.md → architecture/architecture.md} +43 -22
  154. package/docs/{artifact-placement.md → architecture/artifact-placement.md} +26 -23
  155. package/docs/architecture/artifact-versions.md +90 -0
  156. package/docs/{capacity-and-scheduling.md → architecture/capacity-and-scheduling.md} +26 -13
  157. package/docs/{context-engine.md → architecture/context-engine.md} +25 -25
  158. package/docs/{context-working-set.md → architecture/context-working-set.md} +13 -10
  159. package/docs/{dispatch-architecture-rationale.md → architecture/dispatch-architecture-rationale.md} +12 -9
  160. package/docs/{dispatch-typed-intent.md → architecture/dispatch-typed-intent.md} +68 -46
  161. package/docs/{evidence-and-memory.md → architecture/evidence-and-memory.md} +23 -16
  162. package/docs/{middleware-and-components.md → architecture/middleware-and-components.md} +11 -5
  163. package/docs/{model-catalog.md → architecture/model-catalog.md} +40 -17
  164. package/docs/{observability.md → architecture/observability.md} +26 -13
  165. package/docs/{pi-boundary.md → architecture/pi-boundary.md} +24 -11
  166. package/docs/{prompt-envelope-and-tools.md → architecture/prompt-envelope-and-tools.md} +55 -20
  167. package/docs/{provider-adapter-cookbook.md → architecture/provider-adapter-cookbook.md} +35 -24
  168. package/docs/{safety-model.md → architecture/safety-model.md} +20 -15
  169. package/docs/{session-lifecycle.md → architecture/session-lifecycle.md} +8 -5
  170. package/docs/architecture/time-conventions.md +125 -0
  171. package/docs/{trace-store.md → architecture/trace-store.md} +13 -5
  172. package/docs/{tui-design.md → architecture/tui-design.md} +13 -13
  173. package/docs/{worker-dispatch-mechanics.md → architecture/worker-dispatch-mechanics.md} +27 -30
  174. package/docs/{built-in-agents.md → guide/built-in-agents.md} +50 -34
  175. package/docs/{commands-and-modes.md → guide/commands-and-modes.md} +65 -60
  176. package/docs/{configuration-and-targets.md → guide/configuration-and-targets.md} +227 -289
  177. package/docs/guide/configuration-reference.md +1158 -0
  178. package/docs/{environment-variables.md → guide/environment-variables.md} +31 -28
  179. package/docs/{exit-codes-and-output.md → guide/exit-codes-and-output.md} +6 -3
  180. package/docs/{extensions-and-sharing.md → guide/extensions-and-sharing.md} +41 -14
  181. package/docs/{fleet-dispatch.md → guide/fleet-dispatch.md} +39 -43
  182. package/docs/{glossary.md → guide/glossary.md} +14 -11
  183. package/docs/{installation-and-lifecycle.md → guide/installation-and-lifecycle.md} +44 -13
  184. package/docs/guide/panes-and-files.md +290 -0
  185. package/docs/{proactive-memory.md → guide/proactive-memory.md} +79 -66
  186. package/docs/{resource-library.md → guide/resource-library.md} +13 -4
  187. package/docs/{skills-marketplace.md → guide/skills-marketplace.md} +7 -3
  188. package/docs/{tool-usage.md → guide/tool-usage.md} +87 -23
  189. package/docs/{troubleshooting.md → guide/troubleshooting.md} +9 -4
  190. package/docs/{config-knobs-audit.md → history/config-knobs-audit.md} +11 -11
  191. package/docs/{release-cut-checklist.md → history/release-cut-checklist.md} +29 -2
  192. package/docs/{development-pipeline.md → process/development-pipeline.md} +24 -26
  193. package/docs/process/documentation-coverage.md +100 -0
  194. package/docs/process/documentation-guide.md +187 -0
  195. package/docs/{eval-runner.md → process/eval-runner.md} +41 -50
  196. package/docs/{evals-internal.md → process/evals-internal.md} +10 -10
  197. package/docs/{evolution.md → process/evolution.md} +2 -2
  198. package/docs/{fleet-demo-runbook.md → process/fleet-demo-runbook.md} +11 -7
  199. package/docs/{git-commit-provenance.md → process/git-commit-provenance.md} +11 -4
  200. package/docs/{performance-methodology.md → process/performance-methodology.md} +87 -69
  201. package/docs/{scientific-validation.md → process/scientific-validation.md} +4 -4
  202. package/evals/README.md +2 -2
  203. package/package.json +9 -7
  204. package/skills/README.md +46 -37
  205. package/skills/coding/ast-grep/SKILL.md +2 -2
  206. package/skills/coding/coding-standards/SKILL.md +2 -2
  207. package/skills/coding/prototype/SKILL.md +2 -2
  208. package/skills/coding/tdd/SKILL.md +2 -2
  209. package/skills/context/context-handoff/SKILL.md +2 -2
  210. package/skills/context/context-prime/SKILL.md +2 -2
  211. package/skills/git/file-ticket/SKILL.md +2 -2
  212. package/skills/git/fix-issue/SKILL.md +3 -3
  213. package/skills/git/resolve-merge-conflicts/SKILL.md +2 -2
  214. package/skills/git/ship/SKILL.md +2 -2
  215. package/skills/git/worktree-create/SKILL.md +2 -2
  216. package/skills/git/worktree-merge/SKILL.md +2 -2
  217. package/skills/meta/clio-coder-dev/SKILL.md +9 -5
  218. package/skills/meta/clio-coder-dev/evals.md +3 -2
  219. package/skills/meta/clio-coder-test/SKILL.md +102 -95
  220. package/skills/meta/clio-coder-test/evals.md +9 -4
  221. package/skills/meta/clio-coder-test/references/harness.md +100 -124
  222. package/skills/meta/clio-coder-test/references/test-map.md +77 -50
  223. package/skills/meta/credentials/SKILL.md +2 -2
  224. package/skills/meta/find-skills/SKILL.md +2 -2
  225. package/skills/meta/herdr/SKILL.md +2 -2
  226. package/skills/meta/skill-craft/SKILL.md +22 -16
  227. package/skills/planning/architecture/SKILL.md +2 -2
  228. package/skills/planning/backlog/SKILL.md +2 -2
  229. package/skills/planning/prd/SKILL.md +2 -2
  230. package/skills/planning/product-intent/SKILL.md +2 -2
  231. package/skills/planning/tech-spec/SKILL.md +2 -2
  232. package/skills/registry.yaml +62 -62
  233. package/skills/research/arxiv-literature/SKILL.md +2 -2
  234. package/skills/research/experiment-protocol/SKILL.md +2 -2
  235. package/skills/research/scientific-debugging/SKILL.md +2 -2
  236. package/skills/research/scientific-modernization/SKILL.md +2 -2
  237. package/skills/skill-marketplace.json +62 -62
  238. package/skills/workflow/cut-it/SKILL.md +2 -2
  239. package/skills/workflow/design-council/SKILL.md +2 -2
  240. package/skills/workflow/grill-me/SKILL.md +2 -2
  241. package/skills/workflow/workflow-distiller/SKILL.md +2 -2
  242. package/src/cli/args.ts +2 -2
  243. package/src/cli/bootstrap-generate.ts +1 -1
  244. package/src/cli/config-inspect.ts +65 -12
  245. package/src/cli/configure.ts +0 -4
  246. package/src/cli/docs.ts +22 -14
  247. package/src/cli/doctor-naming.ts +5 -5
  248. package/src/cli/doctor-toolchain.ts +3 -3
  249. package/src/cli/eval.ts +1 -2
  250. package/src/cli/extensions.ts +2 -1
  251. package/src/cli/fleet.ts +1 -1
  252. package/src/cli/index.ts +2 -1
  253. package/src/cli/internal-dispatch.ts +3 -4
  254. package/src/cli/panes.ts +19 -5
  255. package/src/cli/run.ts +2 -2
  256. package/src/cli/share.ts +5 -1
  257. package/src/cli/skills-eval.ts +3 -3
  258. package/src/cli/targets.ts +2 -6
  259. package/src/cli/trace.ts +55 -4
  260. package/src/cli/wiki-generate.ts +1 -1
  261. package/src/core/artifact-paths.ts +1 -1
  262. package/src/core/bash-exec.ts +131 -86
  263. package/src/core/bus-events.ts +51 -6
  264. package/src/core/config.ts +5 -1
  265. package/src/core/defaults.ts +7 -4
  266. package/src/core/dispatch-outcome.ts +16 -0
  267. package/src/core/guardrails.ts +10 -49
  268. package/src/core/prompt-hint.ts +9 -0
  269. package/src/domains/agents/builtins/architect.md +2 -3
  270. package/src/domains/agents/builtins/coder.md +3 -2
  271. package/src/domains/agents/builtins/debugger.md +2 -2
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@@ -1,12 +1,12 @@
1
1
  # Commands and Modes
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- > [!TIP]
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- > **Interactive Spec Available:** An interactive dashboard is located at [docs/html/commands_blueprint.html](html/commands_blueprint.html) (Version: 0.4.0).
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+ > **Visual blueprint:** The source checkout includes the complete
4
+ > [Commands and Modes visual reference](https://github.com/iowarp/clio-coder/blob/main/docs/html/commands_blueprint.html).
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5
 
6
-
7
- Clio Coder is a terminal-first alpha harness. This page keeps the command
8
- reference, interaction modes, dispatch surface, verification lanes, and common
9
- operator guidance out of the README so the release entry point stays short.
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+ Clio Coder is a terminal-first coding agent. This page is the detailed command
7
+ reference for interactive sessions, headless runs, dispatch, verification, and
8
+ common operator workflows; the README remains an approachable product and
9
+ onboarding guide.
10
10
 
11
11
  Source of truth: `src/cli/index.ts`, `src/interactive/slash-commands.ts`,
12
12
  `src/domains/dispatch/**`, `src/tools/registry.ts`, and the current test suite.
@@ -33,7 +33,7 @@ For process exit codes, stdout deliverable guarantees, and machine-readable JSON
33
33
  | `clio-coder config [inspect] [--json]` | Print the effective customization graph across settings, context files, rules, skills, prompts, agents, extensions, safety, memory, hooks, and operator profile. |
34
34
  | `clio-coder targets [--json] [--probe] [--target <id>]` | List configured targets, health, auth, runtime, model, and capabilities. |
35
35
  | `clio-coder targets add` | Add a target interactively or through configure flags. |
36
- | `clio-coder targets use <id> [--model <id>] [--orchestrator-model <id>] [--background-model <id>] [--fleet-target <id>] [--fleet-model <id>]` | Point the orchestrator at one target. Without `--fleet-target` the fleet default follows it; with `--fleet-target` the fleet runs on a different node. `--worker-target` and `--worker-model` are accepted aliases from before the worker/fleet rename. |
36
+ | `clio-coder targets use <id> [--model <id>] [--orchestrator-model <id>] [--background-model <id>] [--fleet-target <id>] [--fleet-model <id>]` | Point the orchestrator at one target. Without `--fleet-target` the fleet default follows it; with `--fleet-target` the fleet runs on a different node. |
37
37
  | `clio-coder targets fleet [--json]` | List the configured fleet profiles with their target, runtime, model, and thinking level. `targets workers` is an accepted alias. |
38
38
  | `clio-coder targets profile list\|set\|remove\|rename\|bind\|unbind\|bindings` | Manage named fleet profiles and agent bindings. `clio-coder targets profile <name> <id>` is the short form of `profile set`, and `targets worker` is an accepted alias for `targets profile`. |
39
39
  | `clio-coder targets convert <id> --runtime <runtimeId>` | Convert older local target definitions to a runtime-specific target. |
@@ -51,6 +51,7 @@ For process exit codes, stdout deliverable guarantees, and machine-readable JSON
51
51
  | `clio-coder tools install <id> [--force] [--json]` | Download the platform asset, verify every declared checksum, and atomically vendor it. |
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52
  | `clio-coder tools remove <id>\|--all [--json]` | Remove Clio-vendored copies without touching a program found on `PATH`. |
53
53
  | `clio-coder panes install` | Alias for `clio-coder tools install herdr`. |
54
+ | `clio-coder panes theme` | Print Clio's theme tokens as a herdr `[theme.custom]` block to paste into herdr's `config.toml`; Clio never edits that file itself. See [Panes and the Files Pane](panes-and-files.md). |
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55
  | `clio-coder reset [--state\|--data\|--cache\|--auth\|--config\|--all] [--dry-run] [--force]` | Reset selected Clio Coder state. `--state` is the default level. |
55
56
  | `clio-coder uninstall [--dry-run] [--remove-binary] [--force]` | Remove Clio Coder state and print uninstall guidance. |
56
57
  | `clio-coder upgrade [--dry-run] [--channel=<latest\|beta\|dev>] [--skip-migrations]` | Refresh state metadata, apply migrations, and update npm installs when applicable. |
@@ -69,6 +70,7 @@ For process exit codes, stdout deliverable guarantees, and machine-readable JSON
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  | `clio-coder trace phases <runId> [--db PATH]` | Show one run's recorded phases. |
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71
  | `clio-coder trace tail <runId> [--follow] [--db PATH]` | Tail one run's recorded events; `--follow` streams as they land. |
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72
  | `clio-coder trace procs <runId> [--db PATH]` | Show the processes one run spawned. |
73
+ | `clio-coder trace code-steps <rootId> [--json]` | Show the deterministic code-step records one fleet root wrote (argv, cwd, env names, exit code, duration, output digest, artifact paths). They are files beside the ledger, not rows in the mirror, so `--db` does not apply. |
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74
  | `clio-coder trace prune [--max-age-days N] [--max-bytes N] [--db PATH] [--json]` | Apply the trace-retention policy while protecting queued and running runs; JSON reports the resolved policy, rows, runs and bytes removed, protected runs, and whether vacuum ran. |
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75
  | `clio-coder trace sql <SELECT query> [--db PATH]` | Run one read-only query against the mirror. Only a single `SELECT` or read-only `WITH` statement is accepted; anything else exits 2. |
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76
  | `clio-coder trace ui [--db PATH] [--port N]` | Serve the localhost-only waterfall viewer. The viewer is not part of the published package. |
@@ -114,8 +116,8 @@ For process exit codes, stdout deliverable guarantees, and machine-readable JSON
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116
  | `--tool-profile <name>` | Restrict dispatched-agent tools: `minimal-local`, `science-local`, or `full-agent`. |
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117
  | `--require <capability>` | Require a target capability for dispatch. Repeatable. |
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118
  | `--steer-channel <path>` | Read live steering lines from a FIFO or an appended regular file to steer the active run. |
117
- | `--with-panes` | Activate guest pane integration for this invocation when Clio is already inside a reachable herdr session. It overrides `panes.enabled`. |
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- | `--no-panes` | Disable pane integration for this invocation. It overrides `panes.enabled`. |
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+ | `--with-panes` | Activate guest pane integration for this invocation when Clio is already inside a reachable herdr session. It overrides `interface.panes.enabled`. |
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+ | `--no-panes` | Disable pane integration for this invocation. It overrides `interface.panes.enabled`. |
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121
 
120
122
  `--with-panes` is an explicit first-class launch mode, not permission to start a
121
123
  pane server. Clio confirms `HERDR_ENV=1`, connects to an existing socket, and
@@ -123,7 +125,7 @@ pings it before registering pane tools. The fleet watch pane runs
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125
  `fleet view --watch` against a selection file. Clio writes only the selected run
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  id, while the viewer reads journals itself, so dispatch remains independent of
125
127
  the pane host and a second terminal can use the same journal surface directly.
126
- `panes.enabled: embedded` does not start a host: it is an accepted but
128
+ `interface.panes.enabled: embedded` does not start a host: it is an accepted but
127
129
  unimplemented rung that resolves to no panes, prints a refusal during boot, and
128
130
  is labelled `NOT IMPLEMENTED` in Settings. Use `auto` or `--with-panes` only
129
131
  when Clio is already inside a reachable herdr session.
@@ -167,18 +169,15 @@ The registry table below lists the available interactive slash commands. On a ba
167
169
  | `/quit` | `/quit` | Exit Clio Coder |
168
170
  | `/help` | `/help [query]` | Open the interactive help center showing commands and keys |
169
171
  | `/skill` | `/skill [name] [task]` | Open the Skills Hub or invoke a skill |
170
- | `/library` | `/library [kind]` | Open the Skills Hub on a resource library tab |
171
- | `/prompts` | `/prompts` | List prompt templates |
172
- | `/extensions` | `/extensions` | List installed extensions |
173
- | `/interop` | `/interop` | Review other coding agents detected on this machine |
174
- | `/share` | `/share [runId] \| /share export <path> \| /share import [--dry-run] [--force] <path>` | Share a worker result with the main agent, or export and import Clio archives |
172
+ | `/resources` | `/resources [skills\|prompts\|library [kind]\|extensions [reload]]` | Browse installed resources and private library entries; `extensions reload` commits a new extension generation |
173
+ | `/share` | `/share [runId]` | Share a worker result with the main agent |
174
+ | `/archive` | `/archive export <path> \| /archive import [--dry-run] [--force] <path>` | Export or import a full Clio archive |
175
175
  | `/run` | `/run [--agent-profile <profile>] [--runtime <runtimeId>] [--target <id>] [--model <id>] [--thinking <level>] [--tool-profile <minimal-local\|science-local\|full-agent>] [--require <cap>] [--share] <agent> <task>` | Run a fleet agent |
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176
  | `/delegate` | `/delegate [--share] <agent-id> <task>` | Run an ACP delegation agent |
177
177
  | `/btw` | `/btw <question>` | Ask a side question that never enters the session transcript |
178
178
  | `/oracle` | `/oracle <question>` | Ask a read-only advisor to challenge a question against this session's settled decisions |
179
179
  | `/council` | `/council [--roster <name>] [--rounds <n>] [--synthesis <judge\|vote\|none>] <task>` | Ask a roster of read-only members the same task, with an optional vote or judge synthesis |
180
- | `/agents` | `/agents` | List Clio agents and ACP delegation agents |
181
- | `/targets` | `/targets` | Open Settings → Targets: health, use, connect, probe, remove |
180
+ | `/agents` | `/agents [list\|connect]` | List native and external agents, or review detected external-agent proposals |
182
181
  | `/cost` | `/cost` | Show session token and cost totals |
183
182
  | `/context` | `/context compact [instructions] \| /context recall <ref> \| /context init \| /context refresh \| /context reset` | Context hub: window overlay plus compact, recall, init, refresh, and reset |
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183
  | `/fleet` | `/fleet run [--var <key=value>] <name>` | Open Settings → Fleet, or run a fleet contract with an approval preview |
@@ -186,12 +185,12 @@ The registry table below lists the available interactive slash commands. On a ba
186
185
  | `/tasks` | `/tasks add <text> \| /tasks hand <id> \| /tasks done <id> \| /tasks drop <id>` | Show the session board or manage project operator tasks |
187
186
  | `/memory` | `/memory seed` | Inspect, promote, or seed task memory |
188
187
  | `/view` | `/view [filter] \| /view verify <runId>` | Browse session artifacts and verify receipts |
189
- | `/panes` | `/panes show <run-or-agent> \| /panes open <preset-or-argv> \| /panes close [target]` | Inspect the pane layer, watch a live run in a pane, or open a utility pane |
188
+ | `/panes` | `/panes show <run-or-agent> \| /panes open <preset-or-argv> \| /panes zoom [target] \| /panes close [target]` | Inspect the pane layer, watch a live run in a pane, or open a utility pane (`files`, `logs`, `shell`, `files --once`, or a command); a second open focuses the pane already there |
189
+ | `/files` | `/files [open\|close\|pick]` | Toggle the files pane docked below the session; picks land in the composer as `@` mentions. See [Panes and the Files Pane](panes-and-files.md) |
190
190
  | `/thinking` | `/thinking [level]` | Set the chat thinking level, or open Settings → Orchestrator |
191
191
  | `/output` | `/output [verbosity]` | Set transcript detail (minimal, default, verbose), or open Settings → Terminal |
192
192
  | `/model` | `/model [pattern]` | Open model selector or set a model |
193
- | `/scoped-models` | `/scoped-models` | Open Settings Models: the Alt+J / Alt+K cycle set and favorites |
194
- | `/settings` | `/settings [section]` | Open interactive settings |
193
+ | `/settings` | `/settings [chat\|fleet\|targets\|context\|safety\|interface\|integrations] [group]` | Open interactive settings, optionally at a durable area and UI group |
195
194
  | `/resume` | `/resume` | Resume a past session |
196
195
  | `/new` | `/new` | Start a fresh session |
197
196
  | `/handoff` | `/handoff <goal>` | Hand this session's working state to a fresh session for a stated goal |
@@ -199,6 +198,12 @@ The registry table below lists the available interactive slash commands. On a ba
199
198
  | `/fork` | `/fork` | Fork from an assistant turn |
200
199
  | `/export` | `/export [path]` | Export a self-contained HTML transcript by default; a `.md` path writes Markdown |
201
200
 
201
+ Retired spellings fail closed and print their exact replacement. In particular,
202
+ `/targets` points to `/settings targets`, `/scoped-models` points to
203
+ `/settings chat model-picker`, and `/library`, `/prompts`, and `/extensions`
204
+ point to the corresponding `/resources` subcommand. They never fall through to
205
+ the model as prompt text.
206
+
202
207
  `/context` with no arguments opens the context-window ledger overlay, including
203
208
  the working-set section (policy, evicted items and tokens, events, recalls, churn).
204
209
  The subcommands own the durable project-context noun: `compact` summarizes older
@@ -249,8 +254,8 @@ member's label, target, model, node, round count, and synthesis mode before
249
254
  anything runs. Members are pinned to read-only autonomy and the council tool
250
255
  surface by admission, exactly as they are for a council the model asks for.
251
256
 
252
- `--roster` names a `workers.rosters` entry. Without it the command takes
253
- `workers.rosters.default` when that roster exists, and with neither it refuses
257
+ `--roster` names a `fleet.rosters` entry. Without it the command takes
258
+ `fleet.rosters.default` when that roster exists, and with neither it refuses
254
259
  and names the setting to declare. A roster that is the only one configured is
255
260
  still not the default: seating a council from whichever roster happens to be
256
261
  present would run models the operator never chose. `--rounds` accepts one to
@@ -297,11 +302,11 @@ The `/resume` picker accepts Page Up and Page Down to move by its 12 visible row
297
302
  Only active commands run. Typing anything command-shaped that the registry does
298
303
  not own checks the loaded prompt templates across native and foreign prompt roots.
299
304
  Built-in command names are reserved across interactive and headless modes; a
300
- template with the same basename is omitted from `/prompts` with a collision
305
+ template with the same basename is omitted from `/resources prompts` with a collision
301
306
  diagnostic instead of shadowing a command on one surface and expanding on another.
302
307
  If a matching template is found in an untrusted project root, Clio prints that the
303
308
  prompt template comes from an untrusted project root and directs the operator to set
304
- `skills.trustProjectCompatRoots`, sending nothing to the model. If the token names
309
+ `integrations.projectResources.trustProjectImports`, sending nothing to the model. If the token names
305
310
  neither a command nor a template, it reports `is not a command` and points at `/help`;
306
311
  it is never sent to the model. That covers spellings removed outright, such as
307
312
  `/status` and `/receipts`, as well as ordinary typos. It replaces the earlier
@@ -394,7 +399,7 @@ stable board history and `userTaskId` pickup links survive `/resume` and `/fork`
394
399
  and can be audited from `current.jsonl`. Operator tasks persist separately in
395
400
  `.clio-coder/user-tasks.json`; the overlay can add, hand, finish, or drop them.
396
401
  The model-facing `tasks` tool's session-ledger and inbox bookkeeping is the
397
- documented read-class exception described in [the safety model](safety-model.md):
402
+ documented read-class exception described in [the safety model](../architecture/safety-model.md):
398
403
  calls remain audited as `read` and do not grant workspace mutation authority.
399
404
 
400
405
  The `/decisions` overlay shows completed and cancelled `ask_user` interviews
@@ -411,24 +416,26 @@ and expanded dashboard summarize whether intervention is on, its rules or LLM
411
416
  tier, and current bank size.
412
417
  After `/resume`, Clio offers `/memory seed` when the newest handoff contains a
413
418
  structured snapshot. Seeding is explicit, deduplicated, and unavailable while
414
- `memory.intervention.enabled` is off.
419
+ `context.memory.enabled` is false.
415
420
 
416
- The `/interop` overlay lists the other coding agents Clio found on this machine,
421
+ The `/agents connect` overlay lists the other coding agents Clio found on this machine,
417
422
  grouped `Detected`, `Configured`, and `Declined`. A detected row's detail pane
418
- shows the exact `delegation.agents` entry that connecting it would append, plus
423
+ shows the exact `integrations.externalAgents.entries` entry that connecting it would append, plus
419
424
  the two facts a new peer inherits: `projectContext: none`, so the peer receives
420
425
  the task text and never the project projection, and `toolGovernance:
421
- clio-policy`, so its tool calls are gated by Clio safety. Press `a` to connect
426
+ clio-coder-policy`, so its tool calls are gated by Clio safety. Press `a` to connect
422
427
  one or `d` to decline; the overlay reads the report this process already produced
423
428
  at boot and never probes on a keystroke. Accepting applies to the live session,
424
429
  because `delegation` hot-reloads.
425
430
 
426
- Boot adds at most one line about interop, in the shape `clio: codex detected on
427
- PATH and not configured. Run /interop to review.` It names only agents that are
428
- installed, unconfigured, and undecided, it appears at most once per set of facts,
429
- and it is never emitted in headless or ACP mode. Declining an agent silences it
430
- until its binary version or path changes, at which point it becomes a fresh
431
- proposal.
431
+ Boot adds at most one line about interop, in the current source shape
432
+ `clio-coder: codex detected on PATH and not configured. Run /interop to review.`
433
+ The `/interop` name is retained only as a retired-command tombstone and answers
434
+ `Use /agents connect.`, so operators can open `/agents connect` directly. The
435
+ hint names only agents that are installed, unconfigured, and undecided, appears
436
+ at most once per set of facts, and is never emitted in headless or ACP mode.
437
+ Declining an agent silences it until its binary version or path changes, at which
438
+ point it becomes a fresh proposal.
432
439
 
433
440
  `clio-coder doctor` reports interop and never proposes anything. It emits one
434
441
  `ok` row per detected agent naming its version, its path, and whether it is
@@ -464,8 +471,9 @@ editor reserves and can be rebound through `settings.yaml.keybindings`.
464
471
  | `Alt+T` | Open the session tree navigator (`/tree`). |
465
472
  | `Alt+U` | Toggle the footer dashboard between compact (quiet 2-zone) and expanded (4-zone urgency) layouts. |
466
473
  | `Alt+L` | Open the model and targets selector. |
467
- | `Alt+J` / `Alt+K` | Cycle forward / backward through the scoped model set (when empty, displays a notice directing the operator to `/scoped-models`). |
474
+ | `Alt+J` / `Alt+K` | Cycle forward / backward through the configured model set (when empty, directs the operator to `/settings chat model-picker`). |
468
475
  | `Alt+W` | Toggle the Fleet Runs board (task, run ID, live telemetry, retry, and terminal history). Inside it, `Enter` opens the selected run's live worker detail, `s` steers, and `x` cancels. |
476
+ | `Alt+E` | Toggle the files pane docked below the session in a `--with-panes` session inside herdr; the same as `/files`. Rebind through `clio-coder.files.toggle`. |
469
477
  | `Alt+B` | Open the composite session and operator task board (`/tasks`). Approved application-boundary override of editor word-back. |
470
478
  | `Alt+D` | Open the settled interview decision board (`/decisions`). Approved application-boundary override of editor word-delete. |
471
479
  | `Alt+S` / `Ctrl+Alt+B` | Convert an active attached dispatch to a detached background batch. |
@@ -517,7 +525,7 @@ The `Alt+W` Fleet Runs board makes this control path discoverable: use
517
525
  Up/Down or `j`/`k` to select a run, `s` to close the board and prefill its
518
526
  exact `@<runId> ` steering prefix, and `x` to cancel a live worker or queued
519
527
  retry. A steer first reports `queued`; only the worker's
520
- `clio_steer_received` acknowledgement reports `received`. Single-shot
528
+ `clio_coder_steer_received` acknowledgement reports `received`. Single-shot
521
529
  subprocess runtimes and ACP delegation do not expose a live steering channel
522
530
  and are labeled accordingly.
523
531
 
@@ -528,7 +536,7 @@ Clio Coder operates with a single, unified tool surface. There are no separate t
528
536
  Tool and command execution is governed by:
529
537
  - **Target Capabilities:** What the selected model target actually supports (such as tools, streaming, and vision).
530
538
  - **Safety Net:** Granular rule packs loaded from `damage-control-rules.yaml`, project policies, and protected artifact paths; always on, identical at every autonomy level.
531
- - **Autonomy Mapping:** Once the net passes a call, the level decides whether it runs, asks, or is denied. See [safety-model.md](safety-model.md) for the full matrix.
539
+ - **Autonomy Mapping:** Once the net passes a call, the level decides whether it runs, asks, or is denied. See [safety-model.md](../architecture/safety-model.md) for the full matrix.
532
540
 
533
541
  When an action asks for confirmation, whether from a safety-net rail or from the autonomy level, the call parks and three surfaces say so at once. The transcript row reads `⏸ awaiting approval` with `action ·`, `axis ·`, and `target ·` lines under it; the footer phase pill reads `⏸ confirm`; and a consequence-tier dialog opens with the tool, target, action, authenticated requester, one-shot authority, reversibility, and deny and stop effects. Titles distinguish workspace authority, outward consequences, safety-net confirmation, system changes, and worker escalations. The dialog sits at bottom center with five rows reserved for the composer and footer, and it re-anchors on resize. The composer rail switches to `CONFIRM` and repeats the keys while the prompt owns the keyboard.
534
542
 
@@ -553,6 +561,7 @@ Fleet dispatch runs focused agent recipes through configured targets. The final
553
561
  | `scout` | `explore` / `shadow` | Read-only repository exploration, symbol mapping, and context assembly. |
554
562
  | `researcher` | `research` / `shadow` | Documentation, literature, and web-grounded investigation. |
555
563
  | `provenance` | `operations` / `shadow` | Reading evidence files, receipts, diffs, and telemetry for handoffs. |
564
+ | `oracle` | `plan` / `shadow` | Challenging one question against the session's settled decisions through `/oracle`. |
556
565
  | `context-bootstrap` | `internal` / `internal` | Bootstrap agent behind `clio-coder context init` that inspects the repository and returns `CLIO-CODER.md`. |
557
566
 
558
567
  Examples:
@@ -563,9 +572,11 @@ clio-coder run --agent architect "Plan a minimal change to add JSON output to th
563
572
  clio-coder run --agent verifier "Run tests and confirm the build passes."
564
573
  ```
565
574
 
566
- Shadow agents (`scout`, `researcher`, `provenance`) are internal orchestration
567
- helpers. They appear in `clio-coder agents --all` and the main prompt catalog, but
568
- user-origin `/run` and `clio-coder run --agent` requests are rejected for them.
575
+ Dispatchable shadow helpers (`scout`, `researcher`, `provenance`) appear in
576
+ `clio-coder agents --all`, the full agent catalog, and the compact fleet prompt,
577
+ but user-origin `/run` and `clio-coder run --agent` requests are rejected for
578
+ them. `oracle` also appears in `--all` and the full catalog, but it is deliberately
579
+ excluded from the compact prompt and is reached only through `/oracle`.
569
580
  For broad repository reconnaissance, the operating contract and Scout catalog
570
581
  description steer the model to author a Scout dispatch. The chat harness does
571
582
  not mechanically route the request. A threshold nudge advises Scout delegation
@@ -582,33 +593,23 @@ to execute through the existing engine worker path, the sanctioned Claude Code w
582
593
  | --- | --- |
583
594
  | `npm run ci` | Local and GitHub PR gate: typecheck, lint, skills pin check, build, the deterministic test suite, and the trace-viewer suite. |
584
595
  | `npm run ci:release` | Maintainer release gate: `npm run ci`, then the `check-release` dist and packaging audit. |
585
- | `npm run live:smoke -- --target <id>` | One real headless turn against a configured target. Add `--delegation` for the `opencode` and `copilot` ACP agents. The other operator-run drivers (`live:fleet-dispatch`, `live:tui`, `live:home`) are listed in `benchmarks/internal/README.md`. |
586
596
  | `npm run typecheck` | Strict TypeScript pass. |
587
597
  | `npm run lint` | Biome checks plus `scripts/check-hygiene.ts`, which runs the boundary invariants, the skills pin check, and the README and docs drift rules. |
588
- | `npm run test` | Contract and smoke tests through the sharded runner. |
598
+ | `npm test` | Focused contract and smoke files through plain `node --test`. |
589
599
  | `npm run build` | Production bundle through `tsup`. |
590
600
  | `npm run dev` | `tsup --watch`. |
591
601
  | `npm run clean` | Remove `dist/`. |
592
602
 
593
- Live drivers pick their model with `--target <id>`, naming one of the targets
594
- `clio-coder targets` lists; `--model <wireId>` and `--thinking <level>`
595
- override that target's defaults for the run. The run happens in a scratch Clio
596
- home holding only that target, so nothing touches the operator's real state:
597
-
598
- ```bash
599
- npm run build
600
- npm run live:smoke -- --target local-lmstudio --model qwen3.8-27b
601
- npm run live:smoke -- --target anthropic --delegation
602
- ```
603
-
604
- Live checks cost tokens or local GPU time and are not deterministic CI. They
605
- are useful for OpenAI-compatible local gateways such as llama.cpp, LM Studio
606
- with Dynamo-backed workers, vLLM, and SGLang, plus cloud targets when
607
- credentials are configured.
603
+ Live provider checks cost tokens or local GPU time and are deliberately not
604
+ part of deterministic CI. Maintainers perform them explicitly against an
605
+ isolated Clio home and a named configured target, recording the target, wire
606
+ model id, serving configuration, and result with the release evidence. This is
607
+ the appropriate lane for local gateways such as llama.cpp, LM Studio, vLLM,
608
+ and SGLang, and for cloud targets with operator-provided credentials.
608
609
 
609
610
  ## Environment Variables
610
611
 
611
- Clio Coder's behavior can be customized or overridden using various environment variables (such as `CLIO_CODER_RIGOR`, `CLIO_CODER_HOME`, and guardrail overrides). For the complete, detailed, and maintained inventory of environment variables, please refer to [environment-variables.md](environment-variables.md).
612
+ Clio Coder also reads environment variables for platform paths, diagnostics, lifecycle integration, tests, and process-local behavior such as `CLIO_CODER_RIGOR`. Durable guardrail policy lives only in settings. For the complete maintained inventory, see [environment-variables.md](environment-variables.md).
612
613
 
613
614
  ---
614
615
 
@@ -758,7 +759,11 @@ The Clio TUI has been enhanced to maximize readability, operational focus, and c
758
759
  - **Footer Notification Degradation Ladder:** The footer notification badge reserves the severity head (`glyph count noun`) and `[Alt+X] dismiss` tail first, allocating remaining width to an ellipsized message body. Under narrow terminal constraints, it degrades cleanly down the ladder without clipping action keys.
759
760
  - **Grouped Slash Command Palette:** Typing `/` opens an autocomplete command palette grouped by operational category (`Run`, `Inspect`, `Configure`, `Sessions`) with compact argument hints. Every suggestion is the command's one canonical spelling.
760
761
  - **Voice-First Transcript & Receipts:** User (`› `) and assistant (`✦ `) prose are formatted with a two-cell hanging indent, ensuring wrapped continuation lines remain visually tied to their voice prefix. Tool ledgers maintain full terminal width. Completed turn receipts honor output verbosity (`minimal` none, `default` compact dim `turn · in N · out M`, `verbose` full receipt with call counts, cache reads/writes, reasoning provenance, and verification caveats).
761
- - **Transactional Settings Center:** Open via `/settings` (or deep links `/targets`, `/fleet`, `/scoped-models`, `/thinking`, `/output`). Grouped into `CORE`, `ROUTING`, `RUNTIME`, and `EXPERIENCE` sections. Value edits are transactional: `Enter` opens value pickers/checklists and constructs immutable change plans offering `Apply this session`, `Apply and save globally`, or `Cancel`. Includes the Fleet entity workbench, Targets console table with in-place action drawer, scoped-model checklist, and narrow-terminal drill-down navigation below 72 columns.
762
+ - **Transactional Settings Center:** Open `/settings` or deep-link to one of
763
+ `chat`, `fleet`, `targets`, `context`, `safety`, `interface`, or
764
+ `integrations`. Value edits construct change plans offering `Apply this
765
+ session`, `Apply and save globally`, or `Cancel`; narrow terminals use a
766
+ drill-down layout below 72 columns.
762
767
 
763
768
  ## Overlay and Presentation Conventions
764
769