@iowarp/clio-coder 0.3.9 → 0.4.1

package/skills/meta/{clio-test → clio-coder-test}/SKILL.md

@@ -1,11 +1,17 @@
 ---
-name: clio-test
+name: clio-coder-test
 description: Use when writing or modifying Clio Coder's own source under src/, or verifying a change end-to-end against the real test harness. Covers the three real layers (contracts / smoke / boundaries), choosing which to run for a given change, the mock-provider and ACP-over-stdio harness, and the hot-reload dev loop for picking up latest code. Activate on any src/ edit, before declaring a change verified, or when asked whether Clio still works.
-version: 0.1.4
+triggers:
+  - test Clio Coder
+  - verify a Clio source change
+  - run Clio contract tests
+  - test ACP over stdio
+  - Clio mock provider harness
+version: 0.1.5
 license: Apache-2.0
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
-  source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/clio-test
+  source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/clio-coder-test
   audit: pass
   provenance: designed
   eval-status: scenarios-recorded
@@ -18,7 +24,7 @@ Clio's test suite has exactly three layers: **contracts**, **smoke**, and
 **boundaries**.
 
 For the question of whether a change may leave your machine (commit, push, PR),
-that is `clio-dev`, not this skill. **REQUIRED SUB-SKILL:** `clio-dev` for the
+that is `clio-coder-dev`, not this skill. **REQUIRED SUB-SKILL:** `clio-coder-dev` for the
 local-vs-contribute boundary.
 
 ## Commands

package/skills/meta/{clio-test → clio-coder-test}/evals.md

@@ -1,4 +1,4 @@
-# Evals — clio-test
+# Evals — clio-coder-test
 
 Retrieval + application scenarios. Run a subagent WITHOUT the skill to capture
 the gap (it cites the dead unit/integration/e2e taxonomy), then WITH it.

package/skills/meta/credentials/SKILL.md

@@ -1,7 +1,14 @@
 ---
 name: credentials
 description: Use before running any tool or script that needs an API key, token, or other credential, when a command fails with an auth error, when the user must supply a new secret, or when a secret may have leaked into output. Covers facility surfaces such as kerberos tickets, globus and scheduler tokens, ssh agents, and netrc. Triggers on "API key", "credential", "token", "auth error", "permission denied", "add a secret", "leaked". Not for provider target configuration; use clio-coder auth and target settings.
-version: 0.1.2
+triggers:
+  - API key
+  - credential missing
+  - authentication error
+  - permission denied
+  - add a secret
+  - secret leaked
+version: 0.1.3
 license: Apache-2.0
 allowed-tools:
   - read
@@ -11,7 +18,7 @@ allowed-tools:
   - bash
   - ask_user
   - credential_present
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/credentials
   audit: pass

package/skills/meta/find-skills/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: find-skills
 description: Use when the user asks "is there a skill for X", "find a skill", "install a skill", "add a skill", asks whether a capability exists as an installable skill, or wants to extend the agent with functionality that might already be published. Searches with `clio-coder skills search`, browses the ecosystem read-only, and installs only through `clio-coder skills install`. Not for authoring a new skill; use skill-craft.
-version: 0.1.1
+triggers:
+  - find a skill
+  - is there a skill for this
+  - install a skill
+  - add an agent skill
+  - search the skills marketplace
+version: 0.1.2
 license: Apache-2.0
 allowed-tools:
   - bash
@@ -9,7 +15,7 @@ allowed-tools:
   - read
   - ls
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/find-skills
   audit: pass

package/skills/meta/herdr/SKILL.md

@@ -1,13 +1,19 @@
 ---
 name: herdr
 description: Use when the user explicitly mentions Herdr or asks to launch, drive, or inspect another agent or command in a Herdr pane, tab, or workspace — including starting a second Clio Coder instance and delegating work to it. Requires HERDR_ENV=1. Not for background work a plain shell or dispatch already covers; do not activate merely because a task could benefit from parallelism.
-version: 0.1.0
+triggers:
+  - use Herdr
+  - launch an agent in a Herdr pane
+  - inspect a Herdr agent
+  - start a second Clio Coder instance
+  - drive a command in a Herdr workspace
+version: 0.1.1
 license: Apache-2.0
 allowed-tools:
   - bash
   - read
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/herdr
   audit: pass

package/skills/meta/skill-craft/SKILL.md

@@ -1,12 +1,18 @@
 ---
 name: skill-craft
 description: Use when writing, reviewing, or pruning a SKILL.md — authoring a new skill, editing an installed one, or judging whether a skill's description, body, or length is earning its cost. Triggers on "write a skill", "improve this skill", "why isn't this skill firing", "is this skill too long".
-version: 0.1.1
+triggers:
+  - write a SKILL.md
+  - create a new skill
+  - improve this skill
+  - why isn't this skill firing
+  - prune a skill body
+version: 0.1.3
 license: Apache-2.0
 allowed-tools:
   - read
   - grep
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/meta/skill-craft
   audit: pass
@@ -31,12 +37,23 @@ config dir under `skills/<name>/`. The loader validates on load; check work
 with `clio-coder skills validate`. Frontmatter contract (Agent Skills compatible):
 
 - `name`: lowercase-hyphen, ≤64 chars, must match the folder.
-- `description`: required, ≤1024 chars; its craft is the section below.
+- `description`: required, ≤1024 chars; its craft is the section below. Quote
+  it when it contains ` #` — an unquoted YAML scalar is truncated there.
+- `version` and `license`: required for catalog publication; bump the version
+  on any name or description change so drift detection can tell copies apart.
 - `disable-model-invocation: true`: hides the skill from the agent; only the
   user can activate it.
-- `allowed-tools`: tools the skill body may call.
+- `allowed-tools` / `disallowed-tools`: a *narrowing* declaration, not a
+  grant. While every loaded skill declares `allowed-tools`, the turn's tool
+  surface shrinks to their union; `disallowed-tools` always denies. Neither
+  ever admits a tool the safety level would refuse. Canonical lowercase Clio
+  names only (see skills/README.md, "Claude Code interop").
 - `requires`: `skill:<name>` dependencies; the loader warns when one is
   missing. Reference an installed skill by name instead of restating its job.
+- `clio:`: the reserved publication block (`registry-id`, `source-url`,
+  `audit`, `provenance` designed|adapted|imported with `origin` when not
+  designed, `eval-status`, optional `model-size` and `agents`). Required for
+  catalog skills; approval is judged against it (skills/README.md).
 
 Sibling files (`references/*.md`, `evals.md`, scripts) ride along in the
 folder and load only when the body points at them.

package/skills/planning/architecture/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: architecture
-description: 'Use when an intent (PRD, epic, brief, or idea) needs its engineering approach decided — "how should we build this", "pick the stack", "architecture for this feature". An interactive working session: investigates, proposes 2-3 genuinely different approaches with trade-offs, recommends with reasoning, lets the user decide, and writes a high-level architecture decision doc. Not a task-by-task plan; use cut-it for that. Not a multi-perspective debate; use design-council. Not product intent; use product-intent.'
-version: 0.2.0
+description: 'Use when an intent (PRD, epic, brief, or idea) needs its engineering approach decided — "how should we build this", "pick the stack", "architecture for this feature". An interactive working session: investigates, proposes 2-3 genuinely different approaches with trade-offs, recommends with reasoning, lets the user decide, and writes a high-level architecture decision doc. Not a task-by-task plan; use cut-it for that. Not a multi-perspective debate; use design-council. Not product intent; use product-intent. Not a typed implementation handoff with code-shaped contracts; use tech-spec.'
+triggers:
+  - how should we build this
+  - pick the stack
+  - architecture for this feature
+  - decide the engineering approach
+  - compare architecture options
+version: 0.2.2
 license: Apache-2.0
 allowed-tools:
   - read
@@ -14,7 +20,7 @@ allowed-tools:
   - web_fetch
   - write
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/planning/architecture
   audit: pass

package/skills/planning/backlog/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: backlog
 description: Use when a finished PRD or architecture doc must become a real ticket backlog — "create the stories", "turn this PRD into issues", "build the backlog". Decomposes phases and user stories into small tickets with verifiable acceptance criteria, confirms the list, then creates them as GitHub issues (or in another tracker when an integration exists). Not for local sprint slicing into a SPRINT.md; use cut-it.
-version: 0.2.0
+triggers:
+  - create the stories
+  - turn this PRD into issues
+  - build the backlog
+  - decompose this plan into tickets
+  - create GitHub issues from this architecture
+version: 0.2.1
 license: Apache-2.0
 allowed-tools:
   - read
@@ -10,7 +16,7 @@ allowed-tools:
   - bash
   - tasks
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/planning/backlog
   audit: pass

package/skills/planning/prd/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: prd
 description: Use when the user wants to turn an idea into a product requirements document through a phase-gated interview — each phase locks before the next opens — ending in PRD.md plus per-milestone prompt files ready to drive a coding agent. Triggers on "write a PRD", "spec this out", "help me define this feature/product", or a brain dump that needs structure before planning.
-version: 0.2.1
+triggers:
+  - write a PRD
+  - spec this product out
+  - define this feature
+  - structure this product brain dump
+  - create milestone prompts
+version: 0.2.2
 license: Apache-2.0
 allowed-tools:
   - read
@@ -14,7 +20,7 @@ allowed-tools:
   - write
   - edit
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/planning/prd
   audit: pass

package/skills/planning/product-intent/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: product-intent
 description: Use at the start of a greenfield product effort, when the user wants a problem-first product document — "why are we building this", "write the product thesis", "PRD for this idea". Interviews for the problem, evidence, and a falsifiable hypothesis; writes an intent-only PRD with zero engineering decisions. Not for engineering decisions; use architecture. Not for turning a locked idea into milestone build prompts; use prd.
-version: 0.2.0
+triggers:
+  - why are we building this
+  - write the product thesis
+  - problem-first PRD
+  - define a falsifiable product hypothesis
+  - greenfield product intent
+version: 0.2.1
 license: Apache-2.0
 allowed-tools:
   - read
@@ -12,7 +18,7 @@ allowed-tools:
   - context
   - write
   - ask_user
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/planning/product-intent
   audit: pass

package/skills/planning/tech-spec/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: tech-spec
-description: Write a typed call-stack architecture handoff — code-shaped contracts plus execution flows, implementation-ready for another engineer. User-invoked only.
-version: 0.1.0
+description: Write a typed call-stack architecture handoff — code-shaped contracts plus execution flows, implementation-ready for another engineer. User-invoked only. Not for weighing approaches or deciding the design; use architecture first.
+triggers:
+  - write a tech spec
+  - typed call-stack handoff
+  - code-shaped contracts
+  - implementation-ready technical specification
+  - specify execution flows
+version: 0.1.2
 license: Apache-2.0
 disable-model-invocation: true
 allowed-tools:
@@ -16,7 +22,7 @@ allowed-tools:
   - ask_user
 requires:
   - skill:tdd
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/planning/tech-spec
   audit: pass

package/skills/registry.yaml

@@ -6,131 +6,131 @@ skills:
   # ── coding ──
   - name: ast-grep
     path: coding/ast-grep
-    version: 0.1.0
-    sha256: 24ed3d9490e0923eec1321cb334ae6315194975be1694a243d0d4f45590b586f
+    version: 0.1.1
+    sha256: 29469873f85c3f9e37e065c1968917dac02ea09817d876b7e8c4575d6bdd3c5f
   - name: coding-standards
     path: coding/coding-standards
-    version: 0.1.0
-    sha256: bd906dad6f244c82e3641078964bf69f56b5b36cb692d6e7c09555555451d893
+    version: 0.1.1
+    sha256: f616f7d92f8f4c6dadfe98b99a92981426e0fb250f3391bcfe5b7834c6ecfa31
   - name: prototype
     path: coding/prototype
-    version: 0.2.0
-    sha256: 243258c7ad15a016d930927181912b4282bf84e698c05beaa03b48be1f6fdb66
+    version: 0.2.1
+    sha256: 905911f9651344567a8fd713795024676bb3e1d18f43d3727410b251cf699931
   - name: tdd
     path: coding/tdd
-    version: 0.2.0
-    sha256: da6c7feb5a56d31d111c0e0f1b795f9c0e9012270e4bbc2a35d32b30cbfa9851
+    version: 0.2.1
+    sha256: d9067dede9a63f81bca41487bdab9654eede76da3ef12ef770382b492eacc92c
   # ── context ──
   - name: context-handoff
     path: context/context-handoff
-    version: 0.3.1
-    sha256: 2dc67e24a88607dbedb12163d8afd412421b004df7a845e301accc4e908e18ff
+    version: 0.3.3
+    sha256: 43a70efef5f1914373c1417e6650b8d4db82b8f5aefc7aa6f5c884f3e6b2c36e
   - name: context-prime
     path: context/context-prime
-    version: 0.2.2
-    sha256: 1228302e03b86bcf829ac0016441f408f78b05c4658085d65628cf05fd282f8b
+    version: 0.2.3
+    sha256: 6fb496bf7b5f545e46fa41f10c9964312f1ab2f9d052a3bebaa6c734a70d1746
   # ── git ──
   - name: file-ticket
     path: git/file-ticket
-    version: 0.1.0
-    sha256: 0532ac43ffacbfe3cbc681e68b2cbb7816751d9041b6f1f365e3d43a106a0e91
+    version: 0.1.2
+    sha256: 9c0d73cdf55b8eaff2e86e13e8e8e36a8b7428b9410fd39f7a5d27c547836f82
   - name: fix-issue
     path: git/fix-issue
-    version: 0.1.0
-    sha256: 2c1a7d9c252dd8e0c9512b9610e1c467020fd2948d8d189d594e33e87e2d6fce
+    version: 0.1.2
+    sha256: d2fe942d4ffb30ee9357cd57dd815a75a98322f9d14dca32018960d4bf6c9528
   - name: resolve-merge-conflicts
     path: git/resolve-merge-conflicts
-    version: 0.2.0
-    sha256: 7974a394b560de7e8995a59e7f15fbbb7d6481d2cfdf12238d854cb9278675a0
+    version: 0.2.1
+    sha256: 22de2d0621684c6923001d66206f90d9175a56dc668e82b06942eafe7dd1d45a
   - name: ship
     path: git/ship
-    version: 0.1.0
-    sha256: 58b76f46629562310f833beb2adebe3cc91a078d2d84523608797ee1b53bb445
+    version: 0.1.2
+    sha256: 28081376480038e68ecb27bea99678f887d2deebacc4b928ba3b550f24d641d3
   - name: worktree-create
     path: git/worktree-create
-    version: 0.2.0
-    sha256: 9a22d1e0b5bce8f439f4f757ff47f7ec43a94bb80af87f6834d29644d1334e23
+    version: 0.2.1
+    sha256: f98c7346460291969b91f53fd7f47fbab6ab649e33d921e5047239fa2936e81c
   - name: worktree-merge
     path: git/worktree-merge
-    version: 0.2.0
-    sha256: 407a31fc1e5e21b7aae2af39d09886944272ae8bef5ceed85711ad88122360ed
+    version: 0.2.1
+    sha256: 6a62d4bedd0f3aae1118268ded25e5b155bd4970ab4ec08e5e4553347c9f62f1
   # ── meta ──
-  - name: clio-dev
-    path: meta/clio-dev
-    version: 0.2.0
-    sha256: 386ebfdac9379ebf5630fa7a9af259bb45f473f7d3d679b0a7ef4164f5fc4dea
-  - name: clio-test
-    path: meta/clio-test
-    version: 0.1.4
-    sha256: 90ca1fe7660cd8c3d835801883ebd55d2d17cb652b8585b28ddb82aec642336e
+  - name: clio-coder-dev
+    path: meta/clio-coder-dev
+    version: 0.2.2
+    sha256: 1fed5f9f3de99d9c6db68b1449bc5d89a1c729c560eecf524db764a09efab273
+  - name: clio-coder-test
+    path: meta/clio-coder-test
+    version: 0.1.5
+    sha256: e7f3c83f93c62e54bc6437404ee2f2b95b5bd5541d3fb1a3e8da8fb62354eff4
   - name: credentials
     path: meta/credentials
-    version: 0.1.2
-    sha256: 3730d1492742922981c87643c878b36e927d8745080d3cb99dfa2c0374322c91
+    version: 0.1.3
+    sha256: 92b3eb621d7640b57c44babea634a970284766230cbe2a4d32f08cf385cf4b2e
   - name: find-skills
     path: meta/find-skills
-    version: 0.1.1
-    sha256: c0be6f4198f490930d9370d3a778ae6e64fed0250720f0ff66c08a0e41e838cc
+    version: 0.1.2
+    sha256: 1ef7fb2dbe0585abc24f87146c9c421c5fa2180b9c7ed1a71bfd3fe8b9f12056
   - name: herdr
     path: meta/herdr
-    version: 0.1.0
-    sha256: 147ddba47c4bd99844a896858b5ec483aa3df46fbcfadf8226115ba4bf51456b
+    version: 0.1.1
+    sha256: 511a57533e67aa7046fb0652eb8782c351e677e4a34d947fbe6abffdc8e3e3ed
   - name: skill-craft
     path: meta/skill-craft
-    version: 0.1.1
-    sha256: ec67b2dd6c4684886eed3c0c2204cba783b1d7b691f2234ebad5e9ab58caf754
+    version: 0.1.3
+    sha256: ba6d0c4277e524fd93f5a11c0337e676aee88a9812e9bac3568922f2ad6f0ed1
   # ── planning ──
   - name: architecture
     path: planning/architecture
-    version: 0.2.0
-    sha256: e43e306e49adcc788d71eb534e425e34b13eea8d181a2af38d511308ede39b43
+    version: 0.2.2
+    sha256: 0504f3d4d1d06e4c8947a9366936557391552c5c663106f1c9a41555566cc15c
   - name: backlog
     path: planning/backlog
-    version: 0.2.0
-    sha256: 12c19d24bfac5356089fb225404aa33635b96b4d53bef20751f3389be8680423
+    version: 0.2.1
+    sha256: 5f2b24f2b75af91c4bffceec63334ae07e2048bf908dc7bdbf752f154d297754
   - name: prd
     path: planning/prd
-    version: 0.2.1
-    sha256: bc23b47c94ce40df338b8e775f1992fd602f55636548acbb690fffce2f94efa5
+    version: 0.2.2
+    sha256: 09b3e6c53a87009a8f49760f117948c454ba3e6d4fb59422cbf52cba95277f8c
   - name: product-intent
     path: planning/product-intent
-    version: 0.2.0
-    sha256: 17566702dfb367e9aec1f162a7063b87051af08803be953738a8079f2ab559ed
+    version: 0.2.1
+    sha256: 7c5d87706f4fdec7a27dacd2ba708b1eb957e7bd2b7d21f6f167b4a717616482
   - name: tech-spec
     path: planning/tech-spec
-    version: 0.1.0
-    sha256: 86b3d72a6c2e155e43bdebf6687b039f3a7443ae55fc765814e62241b1e3e47c
+    version: 0.1.2
+    sha256: a938cfc14e1bf2d9d085fc7a37844011396bad97ab8573fb6e8b43e189f16580
   # ── research ──
   - name: arxiv-literature
     path: research/arxiv-literature
-    version: 0.3.0
-    sha256: 08e5c6591e28d6195e4a612b3323bcb63eed93b8e07e54515b6417b11780f8b8
+    version: 0.3.1
+    sha256: 6a33c297e472f57b6094a3a2f494c43473feb338ed9fbda90bb17cee4f5fcb68
   - name: experiment-protocol
     path: research/experiment-protocol
-    version: 0.1.2
-    sha256: 3af25cbcbd1adc37e3a1290cb975e0c2441f347c03148512b38c4f987f3c9c8e
+    version: 0.1.3
+    sha256: 97f632c86717f636f20527eac0a25d85fd8480743a2df54031f3c7440796b355
   - name: scientific-debugging
     path: research/scientific-debugging
-    version: 0.1.2
-    sha256: a9d7e2153c18ec93b00c5b58fd1842201de3c75f7cbea051ae2faac777055520
+    version: 0.1.3
+    sha256: 2bab38911f391947f04d94130f0b02c5398efcd75bf54fa2959cfc669ffc7898
   - name: scientific-modernization
     path: research/scientific-modernization
-    version: 0.2.0
-    sha256: df5aa24fd478c10faac65d0cc9623cfd55ef2405e8f16d3c2d2fee799cf57226
+    version: 0.2.1
+    sha256: adba60897e152c44cb5904b7511d99a61f1899e989e229ff28c5d7bc3caec5fe
   # ── workflow ──
   - name: cut-it
     path: workflow/cut-it
-    version: 0.2.1
-    sha256: f83526535d43137624a9345dbbfbd9de706ccbe464a0aff96dc4a9de2abaaf16
+    version: 0.2.3
+    sha256: d76dc38929d099dba82cef9d77a880b970aeebeaceccd1dd6541ed52d0134852
   - name: design-council
     path: workflow/design-council
-    version: 0.3.0
-    sha256: e02865e1603802acdcb1f3de6c8a43ac7b6f8f1c085f66ed7a5aeae22ab2d8b6
+    version: 0.3.2
+    sha256: 623b9293554147b6335265b781dcdbdcdff55b680ed5f3a0e3840bcaf5bc0773
   - name: grill-me
     path: workflow/grill-me
-    version: 0.3.2
-    sha256: 08f9a165755210dfe942e14fe59803acd19c35ab182b9da10deebdc8554c3f9d
+    version: 0.3.3
+    sha256: 59b1d0a8ab0397c4231d32efc7cf66462d0ddfb57bd7417c904321870e327176
   - name: workflow-distiller
     path: workflow/workflow-distiller
-    version: 0.2.1
-    sha256: 48238593de4877a7b3a4d63e982f9eca84e47f8ec41654dab97da72e9b590ad5
+    version: 0.2.2
+    sha256: 8c765474c34fd4fce1cfb73619cfa289a7850651577d2452228937f1a65ff132

package/skills/research/arxiv-literature/SKILL.md

@@ -1,7 +1,13 @@
 ---
 name: arxiv-literature
 description: Use when the user asks to search arXiv, summarize an arXiv paper, compare papers, find recent research, or build a compact literature survey. Prefer the Researcher shadow agent for noisy multi-paper retrieval; return only citation-ready, source-linked paper cards.
-version: 0.3.0
+triggers:
+  - search arXiv
+  - summarize an arXiv paper
+  - compare these papers
+  - find recent research papers
+  - build a literature survey
+version: 0.3.1
 license: Apache-2.0
 allowed-tools:
   - web_fetch
@@ -11,7 +17,7 @@ allowed-tools:
   - find
   - ls
   - artifact
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/arxiv-literature
   audit: pass

package/skills/research/experiment-protocol/SKILL.md

@@ -1,7 +1,14 @@
 ---
 name: experiment-protocol
 description: Use when running a performance study, numerical comparison, parameter sweep, kernel or solver benchmark, or any change justified by "faster" or "more accurate", and success criteria should be locked before results exist. Pre-registers thresholds, tolerances, environment pins, and verdict conditions into the repository validation contract before any measurement. Triggers on "benchmark", "compare implementations", "optimize", "tolerance", "reproduce results", "parameter sweep". Not for diagnosing a stalled bug; use scientific-debugging.
-version: 0.1.2
+triggers:
+  - benchmark these implementations
+  - pre-register a performance experiment
+  - run a parameter sweep
+  - define numerical tolerances
+  - reproduce these results
+  - compare solver accuracy
+version: 0.1.3
 license: Apache-2.0
 allowed-tools:
   - read
@@ -13,7 +20,7 @@ allowed-tools:
   - context
   - code_nav
   - bash
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/experiment-protocol
   audit: pass

package/skills/research/scientific-debugging/SKILL.md

@@ -1,7 +1,14 @@
 ---
 name: scientific-debugging
 description: Use when debugging has stalled after the first obvious fix, when a failure spans multiple systems, when someone is about to try random changes, or when a scientific or HPC code produces wrong numbers, NaNs, nondeterministic results, or an unexplained performance regression. Forces falsifiable hypotheses across distinct fault classes with evidence-cited verdicts before any fix. Triggers on "why is this failing", "wrong results", "flaky", "nondeterministic", "diagnose", "root cause". Not for designing benchmarks or pre-registered experiments; use experiment-protocol.
-version: 0.1.2
+triggers:
+  - wrong scientific results
+  - nondeterministic HPC code
+  - unexplained performance regression
+  - diagnose NaNs
+  - debug with falsifiable hypotheses
+  - scientific root cause
+version: 0.1.3
 license: Apache-2.0
 allowed-tools:
   - read
@@ -12,7 +19,7 @@ allowed-tools:
   - context
   - code_nav
   - bash
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/scientific-debugging
   audit: pass

package/skills/research/scientific-debugging/evals.md

@@ -42,8 +42,8 @@ if __name__ == "__main__":
     unittest.main()
 PY
 git init -q
-git config user.name "Clio Eval"
-git config user.email "clio-eval@example.invalid"
+git config user.name "Clio Coder Eval"
+git config user.email "eval@clio-coder.local"
 git add diffusion.py tests/test_diffusion.py
 git commit -q -m "add stable weighted mean reference"
 cat > diffusion.py <<'PY'

package/skills/research/scientific-modernization/SKILL.md

@@ -1,7 +1,14 @@
 ---
 name: scientific-modernization
 description: Use when modernizing, porting, rewriting, packaging, accelerating, or replacing established scientific software, especially across languages, build systems, CPU/GPU backends, or maintained forks. Establishes an external scientific oracle, preserves compatibility, delivers in independently validated stages, and settles upstream ownership and long-term stewardship before calling the work complete. Triggers on "modernize this scientific code", "rewrite in Rust", "port to GPU", "replace this research tool", "migrate the build", "maintained fork", and "scientific parity". Not for an isolated benchmark; use experiment-protocol. Not for diagnosing wrong results; use scientific-debugging.
-version: 0.2.0
+triggers:
+  - modernize this scientific code
+  - rewrite this scientific software in Rust
+  - port this solver to GPU
+  - migrate the scientific build system
+  - create a maintained fork
+  - preserve scientific parity
+version: 0.2.1
 license: Apache-2.0
 allowed-tools:
   - read
@@ -13,7 +20,7 @@ allowed-tools:
   - context
   - code_nav
   - bash
-clio:
+clio-coder:
   registry-id: iowarp/clio-coder
   source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/scientific-modernization
   audit: pass