apply-galaxy-workflow-changeset

Apply a reviewed change-set to a concrete Galaxy workflow and emit a galaxy-workflow-draft.gxwf.yml. This Mold plays the topology-settling role the *-to-galaxy-template Molds play in the greenfield pipelines — but it starts from an already-concrete workflow, so its defining job is to change only what the change-set names and carry everything else through untouched.

An edit is a drafty region. The Foundry already drains drafty steps out of a partially-concrete workflow via advance-galaxy-draft-step. So this Mold does not resolve tools or run an edit loop of its own. It represents the whole modified workflow as a draft (see galaxy-workflow-draft-format): untouched steps carried at Resolved tier verbatim, and any edit that introduces or replaces a tool injected as a drafty step + _plan_* for the per-step loop to realize.

What to apply directly vs. defer

• Direct edits (applied inline, no drafty step). remove-step, rewire, relabel / annotate, change-parameter, add-input / remove-input, add-output / expose-output. These need no tool resolution: edit the concrete step/input/output in place and rewire consumers as the change-set dictates. A change-set of purely direct edits yields a draft with draft: false — an immediately concrete workflow, no loop iterations.
• Deferred edits (injected as drafty steps). add-step and replace-tool (when the replacement is a different tool or an unpinned version). Add the step at draft tier with tool_id: TODO (or Identity-pinned when the change-set pinned an id), and record the operation, source evidence, and constraints in _plan_state / _plan_context / _plan_in / _plan_out so advance-galaxy-draft-step can resolve a wrapper and concretize it.

Preserve untouched regions

Every step, input, and output the change-set does not name must survive byte-for-byte: same tool_id, tool_version, tool_state, labels, and connections. Do not reorder, reformat, re-case, or “tidy” an unrelated region — a structural diff of the emitted workflow against the input must touch only the change-set’s targets and their necessary consequences (e.g. rewiring a consumer of a replaced producer). Gratuitous churn is a defect, not a style choice.

Computability and the ledger

An edit can create a gap the connection graph won’t catch: a rewire whose source doesn’t carry what the consumer needs, or a replace-tool whose new tool can’t supply a downstream port. Before handing off, check each edited region is computable from what feeds it. Where you find a gap you can’t wire, append a blocking entry to the open-requirements-ledger naming the edit, the uncomputable output, and the missing evidence — so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late. Never fabricate a connection to make the graph look complete. More generally, carry the ledger: read the entries bearing on the edits and mark resolved the ones the change-set closes.

Hand off

Run draft-validate on the emitted draft (sentinel form, topology, _plan_* placement). On green, hand the draft to advance-galaxy-draft-step, which drains any injected drafty steps and extracts the concrete galaxy-workflow.gxwf.yml. If the change-set was all direct edits, the loop is a no-op and the workflow is already concrete.