@galaxyproject/orbit 0.0.0 → 0.9.0

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/SKILL.md

@@ -0,0 +1,112 @@
+---
+name: advance-galaxy-draft-step
+description: "Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate."
+---
+
+# advance-galaxy-draft-step
+
+Follow the procedure below and use the artifact/reference sections as the runtime contract.
+
+## When To Use
+
+- Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
+
+## Inputs
+
+- Read artifact `galaxy-workflow-draft`. Schema: galaxy-workflow-draft. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. gxformat2 draft (see galaxy-workflow-draft-format) mutated in-place across iterations; topology is fully concrete, individual tool steps may still carry `TODO_*` sentinels and `_plan_*` planning fields.
+- Read artifact `open-requirements-ledger`. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `mature-galaxy-workflow-for-iwc`, `nextflow-summary-to-galaxy-data-flow`, `nextflow-summary-to-galaxy-interface`, `nextflow-summary-to-galaxy-reference-data`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. Carried obligations ledger open-requirements-ledger: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
+
+## Outputs
+
+- Write artifact `galaxy-workflow-draft` as `galaxy-workflow-draft.gxwf.yml`. Format: `yaml`. Schema: galaxy-workflow-draft. Same draft with one additional step concretized (one loop iteration). Once every step is concrete, draft-next-step reports `draft: false` and the harness exits the loop.
+- Write artifact `galaxy-workflow` as `galaxy-workflow.gxwf.yml`. Format: `yaml`. Concrete gxformat2 workflow (`class: GalaxyWorkflow`) extracted from the fully-concretized draft at loop endstate via draft-extract: drafty steps dropped, `_plan_*` planning fields stripped, class promoted. The runnable, testable artifact that downstream Molds (implement-galaxy-workflow-test, validate-galaxy-workflow, run-workflow-test) consume.
+- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
+
+## Required Tools
+
+- **`galaxy-tool-cache`** (galaxy-tool-cache). `npm install -g '@galaxy-tool-util/cli@^1.8.1'`.
+  Ephemeral run: `npx --yes --package @galaxy-tool-util/cli@1.8.1 galaxy-tool-cache`.
+  Check: `galaxy-tool-cache --help | grep -q summarize`.
+  Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli
+- **`gxwf`** (gxwf). `npm install -g '@galaxy-tool-util/cli@^1.8.1'`.
+  Ephemeral run: `npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf`.
+  Check: `gxwf --help | grep -q draft-validate`.
+  Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli
+
+## Load Upfront
+
+- `references/cli/draft-next-step.json`: CLI command reference packaged as a sidecar. Deterministically pick the next drafty step (or report no remaining work). The orchestrator owns the loop oracle so the harness reduces to `while draft: invoke skill`. Use when: at the start of every iteration, before any per-step work.
+- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Read the ledger after each step implementation for a newly appended blocking entry, count the open blocking entries the convergence gate reads, and maintain the topology_repair escalation budget the loop's termination guard depends on.
+- `references/schemas/galaxy-workflow-draft.schema.json`: Schema file copied verbatim into the bundle. In/out contract: the draft this Mold reads and mutates one step per iteration conforms to galaxy-workflow-draft. Cast bundles the JSON Schema alongside the draft-validate CLI checks.
+
+## Load On Demand
+
+- `references/cli/add.json`: CLI command reference packaged as a sidecar. Cache the resolved wrapper for summarization and validation, using its confirmed tool version. Use when: after resolving the wrapper and version, if the shared cache lacks that pin.
+- `references/cli/draft-extract.json`: CLI command reference packaged as a sidecar. At loop endstate, extract the concrete gxformat2 workflow from the fully-concretized draft — drop drafty steps, strip `_plan_*` fields, promote `class` to `GalaxyWorkflow` — and write it as the runnable `galaxy-workflow.gxwf.yml`. Use when: draft-next-step reports `draft: false` (no remaining drafty steps).
+- `references/cli/draft-validate.json`: CLI command reference packaged as a sidecar. Validate the draft and its concrete subset with --concrete --strict-state --json; skipped tool-state checks must fail the gate. Use when: after implementing or modifying the chosen step in the draft.
+- `references/cli/list.json`: CLI command reference packaged as a sidecar. Read a stock tool's cached version when the step plan has no version pin. Use when: in step 2, when the chosen step's tool is a bare/stock id and its concrete version isn't already known from a step-plan pin.
+- `references/notes/galaxy-tool-job-failure-reference.md`: Research note copied verbatim into the bundle. Classify draft-validate diagnostics against wrapper-defined runtime failure semantics so the iteration routes back to the right authoring surface (implementation vs. wrapper choice). Use when: draft-validate fails after a step has been implemented, or when a selected wrapper has explicit failure semantics that may surface at runtime.
+- `references/schemas/galaxy-tool-summary.schema.json`: Schema file copied verbatim into the bundle. Bind the chosen step against the deterministic tool summary manifest emitted by summarize-galaxy-tool — read `parsed_tool` for ports/datatypes and `input_schemas.workflow_step_linked` for valid step `state` shape. Use when: after a wrapper has been resolved for the chosen step and before implementing it.
+
+## Validation
+
+- Validate `galaxy-workflow-draft.gxwf.yml` for artifact `galaxy-workflow-draft` against the galaxy-workflow-draft schema when a validator is available.
+
+## Procedure
+
+Orchestrator skill for the per-step Galaxy authoring loop. One invocation advances the gxformat2 draft by **one** step: pick → resolve a wrapper → summarize the wrapper → implement the step → validate. The harness loop reduces to `while (gxwf draft-next-step <wf>).draft: invoke skill`.
+
+This skill is **single-entry, single-exit**: it owns the loop oracle (draft-next-step) and the per-step validator (draft-validate `--concrete`). Iterations terminate when the draft has no remaining drafty steps; on that terminal call the skill extracts the concrete `galaxy-workflow.gxwf.yml` (via draft-extract) — that promoted-class workflow, not the `-draft` file, is what downstream skills test and run — and the harness then drops out of the loop and proceeds to terminal validation via validate-galaxy-workflow.
+
+### Sequence
+
+Choose a writable tool-cache directory for the run. Pass the same `--cache-dir <dir>` to cache commands, wrapper summarization, and validation.
+
+1. **Pick.** Run draft-next-step. If `draft: false`, the loop is done: run draft-extract to emit the concrete `galaxy-workflow.gxwf.yml` (drafty steps dropped, `_plan_*` stripped, `class` promoted to `GalaxyWorkflow`), then return. Otherwise carry the chosen step id forward.
+2. **Resolve a wrapper.** First check for an existing pin:
+   - **Already resolved in this draft** — find a concrete step with the `tool_id` named by the chosen step's `_plan_*` context or identity pin. Reuse its `tool_id` and `tool_version`, skipping discover-shed-tool for Tool Shed wrappers or cache/version lookup for stock tools. Continue to step 3.
+
+   Otherwise, split on whether the step's tool is a **built-in / stock** Galaxy tool — a bare id with no `owner/repo` path (`Filter1`, `sort1`, `Cut1`, `Show beginning1`, collection ops, `__APPLY_RULES__`):
+   - **Built-in / stock** — the bare id *is* the wrapper identity; it does **not** route through discover-shed-tool (Tool Shed search) or author-galaxy-tool-wrapper. Only its concrete version needs resolving: the shed serves stock tools by bare id, but its TRS version-list endpoint can't auto-resolve the version, so read it from a populated cache via `galaxy-tool-cache list` or take a known pin from the step plan — never hand-guess a stock version. summarize-galaxy-tool then performs the bare-id `add`/`summarize` with that explicit `--tool-version`.
+   - **Tool Shed wrapper** — branch on whether the template already pinned wrapper identity (see the tiers in galaxy-workflow-draft-format):
+     - **Identity-pinned** — `tool_id` is concrete and `tool_version` is `TODO`. Treat the pin as a strong seed: confirm it via discover-shed-tool and resolve the changeset, correcting the `tool_id` only if discovery contradicts the pin (a pinned id is high-confidence template evidence, not a guess to re-derive from scratch).
+     - **Deferred** — `tool_id` is `TODO`. Search fresh: run discover-shed-tool against the step's `_plan_*` context.
+
+     Either way, if no acceptable shed candidate emerges, fall through to author-galaxy-tool-wrapper.
+
+   If the resolved pin is absent from the cache, run add `<tool_id> --tool-version <v> --cache-dir <dir>` before summarization. In `@galaxy-tool-util/cli` 1.10.0, validation also fetches and caches missing metadata unless `--offline` is set; offline validation requires a populated cache.
+3. **Summarize the wrapper.** If step 2 reused a sibling's pin, reuse the cached galaxy-tool-summary for that `tool_id`/`tool_version` pair. Otherwise, invoke summarize-galaxy-tool to produce the summary.
+4. **Implement.** Invoke implement-galaxy-tool-step with the summary and the draft; it resolves the chosen step's remaining `TODO_*` / `_plan_*` slots into a concrete `tool_id` (confirming or correcting any pinned identity), `tool_version`, `state`, and wrapper-determined port names.
+5. **Check computability.** Inspect the open-requirements-ledger for a new `open` blocking entry implement-galaxy-tool-step appended against this step. draft-validate cannot catch this: the connection graph knows ports connect, not what they carry, so the draft validates green even though the step can't run. If such an entry is present, escalate to repair-galaxy-draft-topology for a bounded repair (insert a producer/sub-path or honestly narrow the output), then update the ledger's `topology_repair` budget as the ledger note directs — each escalation must strictly reduce the open blocking-entry count, under a hard cap, and surrender rather than retry once the cap is reached. Then return — the next iteration resumes the loop, realizing any draft-tier steps the repair inserted. With no new blocking entry, continue to validation.
+6. **Validate.** Run draft-validate `<draft> --concrete --strict-state --json --cache-dir <dir>`. `--strict-state` makes skipped tool-state checks fail validation; draft structure and topology checks still run. If metadata is unavailable, resolve the cache or fetch error and retry. Return on exit 0; route other failures using the JSON diagnostics and the rules below.
+
+### Failure routing
+
+`draft-validate --concrete --strict-state --json` failures, after resolving metadata availability, fall into three buckets:
+
+- **Local to the just-implemented step** (sentinel violation, wrong port name, malformed `state`) — re-enter implement-galaxy-tool-step with the diagnostic.
+- **Wrapper-choice mismatch** (selected wrapper cannot satisfy the step's `_plan_*` contract — wrong datatype, missing parameter, incompatible collection shape) — back out to step 2 and pick a different wrapper, either via discover-shed-tool with refined criteria or by escalating to author-galaxy-tool-wrapper.
+- **Earlier-step defect surfaced by the growing concrete projection** (e.g. a connection that looked fine in isolation breaks once a downstream step pulls a previously-deferred port into scope) — flag to the user. The orchestrator does not unwind prior iterations on its own; cross-step rework belongs at the harness level. *Open question: at what threshold should this skill attempt to re-enter implement-galaxy-tool-step for an earlier step versus always escalating?*
+
+These are red-`draft-validate` buckets. The fourth escalation path — a step output uncomputable from its wired inputs — is **not** one of them: the draft validates green there, so it is detected from the ledger in step 5 above, not from a validation failure.
+
+Consult galaxy-tool-job-failure-reference when the wrapper has explicit failure semantics that affect routing — strict-shell behavior, dynamic outputs, or non-default stdio rules can present as wrapper-choice mismatches even when the static shape validates.
+
+### Why orchestrator-shaped
+
+Prior pipelines expressed the iteration as four entries: a `discover-or-author` branch plus `summarize-galaxy-tool`, `implement-galaxy-tool-step`, and `validate-galaxy-step`. Collapsing them into one orchestrator keeps the per-iteration narrative — including the discover-or-author branch and the failure-routing rules — in a single procedural surface that the skill can render coherently. Leaf skills stay independently castable for ad-hoc invocation; only the pipeline shape changes.
+
+## Feedback Mode
+
+- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
+- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
+- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
+- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
+- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
+- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.
+
+## Runtime Notes
+
+- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
+- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
+- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_provenance.json

@@ -0,0 +1,218 @@
+{
+  "provenance_schema_version": 4,
+  "cast_target": "claude",
+  "mold": {
+    "name": "advance-galaxy-draft-step",
+    "path": "content/molds/advance-galaxy-draft-step/index.md",
+    "revision": 7,
+    "content_hash": "ae19f7e5f5ac9434e31302efd88bb5f5db484caf0145951dd27dfe19247f2ea9",
+    "commit": "215b0a4c80c752a9eef2801d46accc4acce88af2"
+  },
+  "cast_at": "2026-09-17T11:40:06.540Z",
+  "refs": [
+    {
+      "kind": "cli-command",
+      "mode": "sidecar",
+      "ref": "[[add]]",
+      "src": "content/cli/galaxy-tool-cache/add.md",
+      "dst": "references/cli/add.json",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "corpus-observed",
+      "purpose": "Cache the resolved wrapper for summarization and validation, using its confirmed tool version.",
+      "trigger": "After resolving the wrapper and version, if the shared cache lacks that pin.",
+      "verification": "Confirm add caches the resolved pin and draft-validate --concrete --strict-state --json validates its state using the same --cache-dir.",
+      "src_hash": "6cb4b61fbdd1aa49a5052abb24020c43bdf57e0360643a65e55b23b42155f561",
+      "dst_hash": "85e3bb884171beb69631186ca6f0f7552e6c6d0721383ab6653e7a32c84a1b71",
+      "source": "deterministic"
+    },
+    {
+      "kind": "cli-command",
+      "mode": "sidecar",
+      "ref": "[[draft-extract]]",
+      "src": "content/cli/gxwf/draft-extract.md",
+      "dst": "references/cli/draft-extract.json",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "hypothesis",
+      "purpose": "At loop endstate, extract the concrete gxformat2 workflow from the fully-concretized draft — drop drafty steps, strip `_plan_*` fields, promote `class` to `GalaxyWorkflow` — and write it as the runnable `galaxy-workflow.gxwf.yml`.",
+      "trigger": "When [[draft-next-step]] reports `draft: false` (no remaining drafty steps).",
+      "verification": "Cast the skill, run the loop to endstate on an IWC-derived draft, confirm draft-extract emits a `class: GalaxyWorkflow` file that passes terminal `gxwf validate` with no `_plan_*` fields or drafty steps.",
+      "src_hash": "f8e9350c96ce005ed5e38deefff6c993824c951784f17f79f7e60d1ad664d8d7",
+      "dst_hash": "c59fbafbe6cf53cd7bcdd867d73b69d078c949c0dfa83abdc084f309793a60aa",
+      "source": "deterministic"
+    },
+    {
+      "kind": "cli-command",
+      "mode": "sidecar",
+      "ref": "[[draft-next-step]]",
+      "src": "content/cli/gxwf/draft-next-step.md",
+      "dst": "references/cli/draft-next-step.json",
+      "used_at": "runtime",
+      "load": "upfront",
+      "evidence": "hypothesis",
+      "purpose": "Deterministically pick the next drafty step (or report no remaining work). The orchestrator owns the loop oracle so the harness reduces to `while draft: invoke skill`.",
+      "trigger": "At the start of every iteration, before any per-step work.",
+      "verification": "Cast the skill, run on a multi-step IWC-derived draft, confirm the orchestrator picks one step per call and exits when draft: false.",
+      "src_hash": "d4fe7945945a57846fe8b168e7bacba04f739de1d86bc613ae6f0e5879ac2f55",
+      "dst_hash": "8638645f5974d8072dc3c63e522b7ab25d562f8d6217ea93b61f0a29f371d6f7",
+      "source": "deterministic"
+    },
+    {
+      "kind": "cli-command",
+      "mode": "sidecar",
+      "ref": "[[draft-validate]]",
+      "src": "content/cli/gxwf/draft-validate.md",
+      "dst": "references/cli/draft-validate.json",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "hypothesis",
+      "purpose": "Validate the draft and its concrete subset with --concrete --strict-state --json; skipped tool-state checks must fail the gate.",
+      "trigger": "After implementing or modifying the chosen step in the draft.",
+      "verification": "Cast the skill, exercise on an IWC-derived draft, confirm both draft-contract diagnostics and concrete-projection diagnostics route back to the step the iteration touched.",
+      "src_hash": "37cded427fbccf49ff19a6fe8b03f9e90857afe556e5db0e51a01402fbf33f1e",
+      "dst_hash": "afa59b0815308a340780247df0548909518564d58352a0c695ceca37a07eee5b",
+      "source": "deterministic"
+    },
+    {
+      "kind": "cli-command",
+      "mode": "sidecar",
+      "ref": "[[list]]",
+      "src": "content/cli/galaxy-tool-cache/list.md",
+      "dst": "references/cli/list.json",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "corpus-observed",
+      "purpose": "Read a stock tool's cached version when the step plan has no version pin.",
+      "trigger": "In step 2, when the chosen step's tool is a bare/stock id and its concrete version isn't already known from a step-plan pin.",
+      "verification": "Cast the skill, populate a cache with a stock tool, run list --json, confirm the reported version is what add's --tool-version uses for that bare id.",
+      "src_hash": "e352306726b54752ad63ac68b2a468d49eb22cebd7b367344ee6b10c8e790434",
+      "dst_hash": "92d336667531c34180db6f75b9fdf87261923c1e85567dce3b21a6d87d9543bd",
+      "source": "deterministic"
+    },
+    {
+      "kind": "research",
+      "mode": "verbatim",
+      "ref": "[[galaxy-tool-job-failure-reference]]",
+      "src": "content/research/galaxy-tool-job-failure-reference/index.md",
+      "dst": "references/notes/galaxy-tool-job-failure-reference.md",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "corpus-observed",
+      "purpose": "Classify [[draft-validate]] diagnostics against wrapper-defined runtime failure semantics so the iteration routes back to the right authoring surface (implementation vs. wrapper choice).",
+      "trigger": "When draft-validate fails after a step has been implemented, or when a selected wrapper has explicit failure semantics that may surface at runtime.",
+      "src_hash": "bf6530fca24f40780836e92d8d263f789038a6e0a722351ab8e8c9aa42646e2c",
+      "dst_hash": "bf6530fca24f40780836e92d8d263f789038a6e0a722351ab8e8c9aa42646e2c",
+      "source": "deterministic"
+    },
+    {
+      "kind": "research",
+      "mode": "verbatim",
+      "ref": "[[open-requirements-ledger]]",
+      "src": "content/research/open-requirements-ledger/index.md",
+      "dst": "references/notes/open-requirements-ledger.md",
+      "used_at": "runtime",
+      "load": "upfront",
+      "evidence": "hypothesis",
+      "purpose": "Read the ledger after each step implementation for a newly appended blocking entry, count the open blocking entries the convergence gate reads, and maintain the topology_repair escalation budget the loop's termination guard depends on.",
+      "verification": "Promote after a run where a blocking entry appended by implement is detected here and drives an escalation that strictly reduces the open count.",
+      "src_hash": "e1d5e3a4d6d650af5b2efc4703fe6f79bb4d0cc12e6cd14e841c5b91df122ea0",
+      "dst_hash": "e1d5e3a4d6d650af5b2efc4703fe6f79bb4d0cc12e6cd14e841c5b91df122ea0",
+      "source": "deterministic"
+    },
+    {
+      "kind": "schema",
+      "mode": "verbatim",
+      "ref": "[[galaxy-tool-summary]]",
+      "src": "package://@galaxy-foundry/gxwf-foundry#galaxyToolSummarySchema",
+      "dst": "references/schemas/galaxy-tool-summary.schema.json",
+      "used_at": "runtime",
+      "load": "on-demand",
+      "evidence": "corpus-observed",
+      "purpose": "Bind the chosen step against the deterministic tool summary manifest emitted by [[summarize-galaxy-tool]] — read `parsed_tool` for ports/datatypes and `input_schemas.workflow_step_linked` for valid step `state` shape.",
+      "trigger": "After a wrapper has been resolved for the chosen step and before implementing it.",
+      "src_hash": "bf77d0735410fa0028bc9bea08edaff3016580508bf27851fdcae65d038f2d94",
+      "dst_hash": "bf77d0735410fa0028bc9bea08edaff3016580508bf27851fdcae65d038f2d94",
+      "source": "deterministic"
+    },
+    {
+      "kind": "schema",
+      "mode": "verbatim",
+      "ref": "[[galaxy-workflow-draft]]",
+      "src": "package://@galaxy-tool-util/schema#galaxyWorkflowDraftJsonSchema",
+      "dst": "references/schemas/galaxy-workflow-draft.schema.json",
+      "used_at": "runtime",
+      "load": "upfront",
+      "evidence": "cast-validated",
+      "purpose": "In/out contract: the draft this Mold reads and mutates one step per iteration conforms to [[galaxy-workflow-draft]]. Cast bundles the JSON Schema alongside the [[draft-validate]] CLI checks.",
+      "license": "MIT",
+      "license_file": "LICENSES/galaxy-tool-util-ts.LICENSE",
+      "src_hash": "86822b6bf4c11ba1d9eaa12d9e442db7f7d28b2734a2daddf62b5cdd2f1f75aa",
+      "dst_hash": "86822b6bf4c11ba1d9eaa12d9e442db7f7d28b2734a2daddf62b5cdd2f1f75aa",
+      "source": "deterministic",
+      "license_file_hash": "383450c494c01c466bcf22df102540a39ac89da50563fd7be686ba06772f96b3"
+    }
+  ],
+  "artifacts": {
+    "produces": [
+      {
+        "id": "galaxy-workflow-draft",
+        "kind": "yaml",
+        "default_filename": "galaxy-workflow-draft.gxwf.yml",
+        "schema": "[[galaxy-workflow-draft]]",
+        "description": "Same draft with one additional step concretized (one loop iteration). Once every step is concrete, [[draft-next-step]] reports `draft: false` and the harness exits the loop."
+      },
+      {
+        "id": "galaxy-workflow",
+        "kind": "yaml",
+        "default_filename": "galaxy-workflow.gxwf.yml",
+        "description": "Concrete gxformat2 workflow (`class: GalaxyWorkflow`) extracted from the fully-concretized draft at loop endstate via [[draft-extract]]: drafty steps dropped, `_plan_*` planning fields stripped, class promoted. The runnable, testable artifact that downstream Molds ([[implement-galaxy-workflow-test]], [[validate-galaxy-workflow]], [[run-workflow-test]]) consume."
+      },
+      {
+        "id": "open-requirements-ledger",
+        "kind": "yaml",
+        "default_filename": "open-requirements.ledger.yml",
+        "description": "Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact."
+      }
+    ],
+    "consumes": [
+      {
+        "id": "galaxy-workflow-draft",
+        "description": "gxformat2 draft (see [[galaxy-workflow-draft-format]]) mutated in-place across iterations; topology is fully concrete, individual tool steps may still carry `TODO_*` sentinels and `_plan_*` planning fields.",
+        "inherited_schema": "[[galaxy-workflow-draft]]",
+        "producers": [
+          "advance-galaxy-draft-step",
+          "apply-galaxy-workflow-changeset",
+          "cwl-summary-to-galaxy-template",
+          "freeform-summary-to-galaxy-template",
+          "implement-galaxy-tool-step",
+          "nextflow-summary-to-galaxy-template",
+          "repair-galaxy-draft-topology"
+        ]
+      },
+      {
+        "id": "open-requirements-ledger",
+        "description": "Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.",
+        "producers": [
+          "advance-galaxy-draft-step",
+          "apply-galaxy-workflow-changeset",
+          "compare-against-iwc-exemplar",
+          "cwl-summary-to-galaxy-data-flow",
+          "cwl-summary-to-galaxy-interface",
+          "cwl-summary-to-galaxy-template",
+          "freeform-summary-to-galaxy-data-flow",
+          "freeform-summary-to-galaxy-interface",
+          "freeform-summary-to-galaxy-template",
+          "implement-galaxy-tool-step",
+          "interview-to-galaxy-workflow-changeset",
+          "mature-galaxy-workflow-for-iwc",
+          "nextflow-summary-to-galaxy-data-flow",
+          "nextflow-summary-to-galaxy-interface",
+          "nextflow-summary-to-galaxy-reference-data",
+          "nextflow-summary-to-galaxy-template",
+          "repair-galaxy-draft-topology"
+        ]
+      }
+    ]
+  }
+}

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_required_tools.json

@@ -0,0 +1,33 @@
+[
+  {
+    "tool": "galaxy-tool-cache",
+    "origin": "npm",
+    "package": "@galaxy-tool-util/cli",
+    "package_version": "^1.8.1",
+    "invoke": "galaxy-tool-cache",
+    "invoke_fallback": "npx --yes --package @galaxy-tool-util/cli@1.8.1 galaxy-tool-cache",
+    "availability_check": "galaxy-tool-cache --help | grep -q summarize",
+    "docs_url": "https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli",
+    "source": "implied",
+    "implied_by": [
+      "galaxy-tool-cache add",
+      "galaxy-tool-cache list"
+    ]
+  },
+  {
+    "tool": "gxwf",
+    "origin": "npm",
+    "package": "@galaxy-tool-util/cli",
+    "package_version": "^1.8.1",
+    "invoke": "gxwf",
+    "invoke_fallback": "npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf",
+    "availability_check": "gxwf --help | grep -q draft-validate",
+    "docs_url": "https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli",
+    "source": "implied",
+    "implied_by": [
+      "gxwf draft-extract",
+      "gxwf draft-next-step",
+      "gxwf draft-validate"
+    ]
+  }
+]

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/_verify.json

@@ -0,0 +1,4 @@
+{
+  "verify_schema_version": 1,
+  "entries": []
+}

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/add.json

@@ -0,0 +1,50 @@
+{
+  "type": "cli-command",
+  "tool": "galaxy-tool-cache",
+  "command": "add",
+  "summary": "Fetch a tool from the Tool Shed (shed-path or bare/stock id) and cache its ParsedTool locally for later summarize/schema.",
+  "source_path": "content/cli/galaxy-tool-cache/add.md",
+  "source_revision": 2,
+  "package": "@galaxy-tool-util/cli",
+  "description": "Fetch a tool from the ToolShed (shed-path or bare/stock ID) and cache it",
+  "synopsis": "galaxy-tool-cache add [options] <tool_id>",
+  "args": [
+    {
+      "raw": "tool_id",
+      "name": "tool_id",
+      "required": true,
+      "variadic": false,
+      "description": "Tool ID: shed path (owner/repo/tool), TRS ID, or bare/stock ID (e.g. Filter1)"
+    }
+  ],
+  "options": [
+    {
+      "flags": "--tool-version <ver>",
+      "name": "toolVersion",
+      "description": "Tool version",
+      "takesArgument": true,
+      "argumentPlaceholder": "<ver>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--cache-dir <dir>",
+      "name": "cacheDir",
+      "description": "Cache directory",
+      "takesArgument": true,
+      "argumentPlaceholder": "<dir>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--galaxy-url <url>",
+      "name": "galaxyUrl",
+      "description": "Alternate Galaxy source, tried after the ToolShed",
+      "takesArgument": true,
+      "argumentPlaceholder": "<url>",
+      "optionalArgument": false,
+      "negatable": false
+    }
+  ],
+  "body": "# `galaxy-tool-cache add`\n\nFetch a single tool by id from the Tool Shed and cache its parsed wrapper into the local cache directory. This is the cache-population precondition for summarize-galaxy-tool: `summarize` reads an already-cached pin and fails if the entry is missing, so `add` runs first.\n\n`<tool_id>` is a full Tool Shed path (e.g. `toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search`), a TRS id, **or a bare/stock id** for a built-in Galaxy tool (`Filter1`, `sort1`, `Cut1`, `Show beginning1`, collection ops). The Tool Shed serves stock tools too, so bare ids resolve against the same shed source — there is no separate Galaxy lookup in the default path. Pin the exact wrapper with `--tool-version` so the cache key matches the discovery pin from discover-shed-tool.\n\nTo cache every tool a draft references in one pass instead of pin-by-pin, use `populate-workflow` (scans a `.ga`/`.gxwf.yml`); the loop driver advance-galaxy-draft-step uses that form.\n\n## Output\n\nNo manifest on stdout — the effect is a populated `--cache-dir`. `add` writes the fetched ParsedTool into the cache keyed by tool id + version; `summarize` and `schema` read it from there. Stdout reports the cached tool (`Cached: <name> (<id> v<version>)`); a hard error on an unresolvable id exits non-zero.\n\n## Examples\n\n```bash\n# Tool Shed wrapper, pinned by discovery\ngalaxy-tool-cache add toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search \\\n  --tool-version 0.11.0+galaxy3 --cache-dir ~/.cache/gxwf\n\n# Stock/built-in tool by bare id (resolves against the shed)\ngalaxy-tool-cache add \"Show beginning1\" --tool-version 1.0.2 --cache-dir ~/.cache/gxwf\n```\n\n## Gotchas\n\n- `add` is per-pin. Caching the search hit without `--tool-version` may resolve to a different revision than the discovery pin — pass the version explicitly.\n- **Stock ids need an explicit `--tool-version`.** Auto-version discovery routes through the shed's TRS version-list endpoint (`…/api/ga4gh/trs/v2/tools/<id>/versions`), which currently 500s, so a bare `add Filter1` fails with \"Failed to fetch tool\". Pass the concrete version (`add Filter1 --tool-version 1.1.1`); never hand-guess a stock version — confirm it (e.g. from a populated cache via `list`, or a known pin). Requires `@galaxy-tool-util/cli >= 1.8.1`.\n- Network-bound: requires Tool Shed (or `--galaxy-url`) reachability. Offline runs must reuse a pre-populated `--cache-dir`.\n- Pass the same `--cache-dir` to `add`, `summarize`, and `schema` — they share one cache; `summarize`/`schema` read what `add` wrote."
+}

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/draft-extract.json

@@ -0,0 +1,51 @@
+{
+  "type": "cli-command",
+  "tool": "gxwf",
+  "command": "draft-extract",
+  "summary": "Extract the concrete subset of a draft workflow: trim drafty steps, strip `_plan_*`, promote class when fully resolved.",
+  "source_path": "content/cli/gxwf/draft-extract.md",
+  "source_revision": 1,
+  "package": "@galaxy-tool-util/cli",
+  "description": "Extract the concrete subset of a draft workflow (drop drafty steps, strip _plan_* fields, promote class when fully concrete)",
+  "synopsis": "gxwf draft-extract [options] <file>",
+  "args": [
+    {
+      "raw": "file",
+      "name": "file",
+      "required": true,
+      "variadic": false,
+      "description": "Draft workflow file (.gxwf.yml)"
+    }
+  ],
+  "options": [
+    {
+      "flags": "-o, --output <file>",
+      "name": "output",
+      "short": "-o",
+      "description": "Write extracted workflow to file (default: stdout)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<file>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--report-json [file]",
+      "name": "reportJson",
+      "description": "Write extraction report JSON (drops, rewrites, class flip) — to file or stdout if omitted",
+      "takesArgument": true,
+      "argumentPlaceholder": "[file]",
+      "optionalArgument": true,
+      "negatable": false
+    },
+    {
+      "flags": "--format <fmt>",
+      "name": "format",
+      "description": "Force input format: format2 (default; native is rejected)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<fmt>",
+      "optionalArgument": false,
+      "negatable": false
+    }
+  ],
+  "body": "# `gxwf draft-extract`\n\nTransform a draft workflow into its already-concretized subset. Pipes three operations from `@galaxy-tool-util/schema` in order:\n\n1. `extractConcreteSubset` — drop steps that still carry `TODO_*` or `_plan_*`; cascade through dead `in:` deps; rewrite multi-source inputs to the surviving subset; fall back to `default:` when a single source dies; recurse into draft subworkflows; drop orphan workflow outputs.\n2. `stripPlanFields` — remove `_plan_*` planning fields from every surviving step and from the workflow root.\n3. `promoteFullyConcreteDrafts` — flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any (sub)workflow now carrying zero TODOs and zero `_plan_*`. Inner draft with remaining work blocks outer promotion.\n\nNative (.ga) input is rejected — drafts are format2-only. Output format is inferred from the `-o` extension (`.ga` / `.json` → native JSON; otherwise format2 YAML) or, when emitting to stdout, matches the input format. Promoted from the earlier hidden `_draft-extract` command — same behavior, same flags, now first-class in `gxwf --help`.\n\n## Output\n\nBy default, the trimmed workflow is written to stdout. With `-o <file>`, written to that file. `--report-json [file]` emits a `SingleDraftExtractReport` sidecar with `dropped_steps`, `dropped_outputs`, `rewritten_step_inputs`, and the post-extract class.\n\n## Examples\n\n```bash\ngxwf draft-extract workflow.gxwf.yml > concrete.gxwf.yml\ngxwf draft-extract workflow.gxwf.yml -o concrete.gxwf.yml --report-json report.json\ngxwf draft-extract workflow.gxwf.yml -o concrete.ga\ngxwf draft-extract workflow.gxwf.yml | gxwf validate -\n```\n\n## Exit codes\n\n- `0` — input parsed and the extract pipeline ran (including the empty-extract case).\n- `2` — parse / read failure, native input rejected, or a stdout-sink collision between the workflow output and `--report-json=-` both targeting stdout.\n\n## Gotchas\n\n- This command is **a transformation, not a validator**. To validate the concrete subset against full `gxformat2` rules, pipe to validate (or invoke draft-validate with `--concrete`, which runs the same pipeline internally).\n- The trimmed workflow may still be `class: GalaxyWorkflowDraft` — promotion only fires when zero TODOs and zero `_plan_*` remain anywhere (including inside draft subworkflows).\n- `extractConcreteSubset` operates as a fixpoint and is deterministic per-level: drops within a level sort by `(round, path)`; inner-level drops follow their containing surviving subworkflow in source iteration order.\n- Outer subworkflow steps are never shrunk in v1 — inner workflows shrink in place. A drafty step at the outer level either survives whole or is dropped whole.\n- Use `--report-json` whenever a cast skill needs to surface which steps were trimmed (e.g., to explain why a downstream test fails on a workflow that \"validates fine but is missing the step you asked about\")."
+}

package/extensions/orbit/vendor/skills/advance-galaxy-draft-step/references/cli/draft-next-step.json

@@ -0,0 +1,42 @@
+{
+  "type": "cli-command",
+  "tool": "gxwf",
+  "command": "draft-next-step",
+  "summary": "Pick the next drafty step a harness should work on, or report no remaining work; deterministic topological + alphabetical tiebreak.",
+  "source_path": "content/cli/gxwf/draft-next-step.md",
+  "source_revision": 1,
+  "package": "@galaxy-tool-util/cli",
+  "description": "Pick the next step a downstream agent should work on (or report no remaining work)",
+  "synopsis": "gxwf draft-next-step [options] <file>",
+  "args": [
+    {
+      "raw": "file",
+      "name": "file",
+      "required": true,
+      "variadic": false,
+      "description": "Draft workflow file (.gxwf.yml)"
+    }
+  ],
+  "options": [
+    {
+      "flags": "--format <fmt>",
+      "name": "format",
+      "description": "Force input format: format2 (default; native is rejected)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<fmt>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--output-format <fmt>",
+      "name": "outputFormat",
+      "description": "Output format: json (default) or markdown",
+      "takesArgument": true,
+      "argumentPlaceholder": "<fmt>",
+      "optionalArgument": false,
+      "negatable": false,
+      "defaultValue": "json"
+    }
+  ],
+  "body": "# `gxwf draft-next-step`\n\nDeterministic next-step picker for the per-step authoring loop. Wraps `nextDraftStep` from `@galaxy-tool-util/schema`. Native (.ga) input is rejected — drafts are format2-only.\n\nThe harness loop reads as: `while (next = gxwf draft-next-step <wf>).draft: invoke per-step skill on next.step`.\n\n## Output\n\nDefault output is pretty JSON — the agent-loop wire format. Same input → byte-identical output. `--output-format markdown` renders a human-glance checklist instead.\n\nJSON fields:\n\n- `draft` (bool) — `true` while a drafty step remains, `false` at the terminal cases below.\n- `step` (string array) — the picked step's **path**: a single id at top level (`[\"merge assembled transcripts\"]`), or the full path through containing subworkflow steps when the pick is nested. The leaf (last element) is the step to work on.\n- `work` (string array) — the chosen step's remaining `TODO[...]` sentinels followed by its `_plan_*` fields, in checklist order.\n\nAt the terminal cases the object is just `{ \"draft\": false }` — no `step` or `work` keys.\n\nTwo terminal cases both surface as `draft: false`:\n\n- The workflow's class is already `GalaxyWorkflow` (concretization complete, class promoted).\n- The class is still `GalaxyWorkflowDraft` but every step is fully resolved (no `TODO_*`, no `_plan_*`). The harness's next move is draft-extract (which calls `promoteFullyConcreteDrafts` to flip the class) followed by terminal validate.\n\n## Examples\n\n```bash\ngxwf draft-next-step workflow.gxwf.yml\ngxwf draft-next-step workflow.gxwf.yml --output-format markdown\n```\n\nHarness loop sketch:\n\n```bash\nwhile [ \"$(gxwf draft-next-step workflow.gxwf.yml | jq -r .draft)\" = \"true\" ]; do\n  step=$(gxwf draft-next-step workflow.gxwf.yml | jq -r '.step | last')\n  # invoke per-step skill on step, which mutates workflow.gxwf.yml in place\ndone\n```\n\n## Gotchas\n\n- Pick order is **topological** (a step waits until its `in:` sources are concretized) with **alphabetical tiebreak** on step id at the same level. Same input across runs returns the same pick — safe to call repeatedly without state.\n- Descends into draft subworkflows; the returned `step` array is the full path through containing subworkflow steps (leaf last).\n- A `draft: false` result does **not** mean the workflow has passed validate yet. It means the per-step authoring loop is done; the harness still owns the promote + terminal-validate pass.\n- This command does not mutate the workflow file. It's a pure observer.\n- Insertion order of step dicts does not affect output — semantically equal workflows produce identical picks."
+}