[ctawiah]

Context

Phase 1 linked a prompt to a repository file through a ref entry in the front matter of its managed file, with one plain Markdown adapter. The .ref.yaml descriptors in the next pull requests replace that design.

What changes

• Remove the Phase 1 reference format, the plain Markdown adapter, and the ref front matter field.
• Remove the Phase 1 sync prompts link command and its planner and executor branches.
• Remove the Phase 1 reference rows from the lock and the acceptance tests that covered them.

Design notes

• This change only removes code. The next pull request adds the shared projection model that the descriptors build on.

Review focus

• Does any Phase 1 reference path remain in the planner or the local store?

Verification

• make build
• go test ./...
• golangci-lint run ./...

Related changes

1. This PR: Phase 1 reference removal
2. feat(sync): add projection and problem core #987: projection and problem core
3. feat(sync): add the adapter core and the Markdown adapter #988: adapter core and Markdown
4. feat(sync): add the structured document adapters #989: structured adapters
5. feat(sync): add the Python adapter #991: Python adapter
6. feat(sync): add the TypeScript and JavaScript adapters #992: TypeScript and JavaScript adapters
7. feat(sync): add source descriptor storage #993: descriptor storage
8. feat(sync): compile and publish repository sources #994: compile and publish
9. feat(sync): detach descriptor-backed sources #1003: descriptor detach
10. feat(sync): prepare repository source links #997: link preparation
11. feat(sync): integrate repository sources with planning and link #995: planning and link
12. feat(sync): add the link commands #998: link commands

🤖 Generated with Claude Code

---

Note

Overview
This PR removes the Phase 1 “linked prompt” model so sync no longer supports variation wrappers that point at external repo files via YAML ref front matter. It is deletion-only groundwork before .ref.yaml descriptors land in follow-up PRs.

CLI and actions: ldcli sync prompts link is gone, along with LinkAction, linkTarget, and runner wiring that created a linked variation then ran sync.

Deleted packages: internal/sync/link (link workflow), internal/sync/reference and the plain-markdown adapter, and internal/sync/local/reference.go (path validation and reading linked files).

Local workspace: Variations are inline only—compile no longer merges content from referenced files; VariationFile / front matter drop Ref; ReplaceVariations no longer rewrites external prompt files on pull; SourceFiles and watch tests no longer treat repo paths outside .launchdarkly as sync inputs.

Planner / executor / lock: Manifest entries no longer store ref; SetRefs, planRestore, and post-sync ref recording are removed. Pull-to-local no longer passes restoreRef.

Tests: Flag inventories, acceptance scenarios for linked push/pull/detach/restore, and link-specific unit tests are removed or trimmed accordingly.

Note for reviewers: Stale comments in watch.go / compile.go still mention linked files; behavior now follows managed files only via SourceFiles.

^{Reviewed by Cursor Bugbot for commit 140c3bc. Bugbot is set up for automated code reviews on this repo. Configure here.}