Claude Code's (and Copilot's) native plugin installer has zero awareness of .apm/ nesting -- it convention-scans only flat skills/, agents/, commands/, hooks.json at each plugin's root. Confirmed via strings on the installed claude binary and live installs of git@holocron/gitea@holocron/kyberforge@ holocron, all reporting Skills(0) Agents(0) Hooks(0) post ADR-0015's apm conversion. Root cause (apm_cli/core/plugin_manifest.py): apm's plugin.json compiler deliberately strips skills/agents/commands keys, assuming the host already auto-discovers those convention directories -- it has no model of .apm/ being host-visible at all. Separately, apm's own bundle exporter (apm_cli/bundle/plugin_exporter.py, behind `apm pack --format plugin`) implements the correct .apm/ -> flat mapping, but only ever targeted build/<name>-<version>/, a path nothing in marketplace.json's source: points at. scripts/sync-plugin-content.sh wraps that bundle exporter and copies its agents/, skills/, commands/, instructions/, extensions/, and merged hooks.json back into each plugin's own root as a second tracked compiled-output category -- same governance status as .claude-plugin/plugin.json: generated from .apm/, never hand-edited. tests/ subdirectories are excluded from the mirror (dev fixtures, not host-visible runtime content; several hardcode a relative repo-root walk-up sized for the .apm/-nested depth, which breaks when duplicated one level shallower). Applied for real across all 6 plugins and verified two ways: `claude plugin validate --strict` passes on every real plugin directory, and a live `claude --plugin-dir <path> -p "list skills/agents"` behavioral test confirms content is now actually discovered. Also, from the same issue #90 review round: - scripts/check-manifests.sh pointed at each plugin's root-level plugin.json (checking skills/hooks/mcpServers/agents pointer fields) -- that file was a stale near-duplicate of .claude-plugin/plugin.json nothing else read or wrote, now deleted across all 6 plugins. check-manifests.sh is rewritten to validate .claude-plugin/plugin.json instead, and drops the pointer-field checks entirely (nothing to check -- those fields are correctly absent by design). Content-presence drift is now check-plugin-content-sync's job, a new pre-push hook wired in .pre-commit-config.yaml. docs/adr/0017 records the root cause and decision in full, including two rejected alternatives (patching plugin.json's path fields directly -- apm's compiler strips them on every run; pointing marketplace.json at apm pack's build/ output -- a version-suffixed non-source directory nothing can install from without an extra build step). ADR-0015 and CONTEXT.md are updated to point at it. Refs: #90
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Canonical call sequences
Push a file to a new branch, then open a PR
1. get_repository_tree or get_file_contents on the base branch — only needed if the
new file is actually replacing an existing one; skip for a brand-new path.
2. create_or_update_file
owner, repo
path: "docs/example.md"
content: "<base64-encoded content>"
message: "docs: add example"
branch_name: "main"
new_branch_name: "feat/add-example" ← branches off before the commit lands
(sha omitted — this is a new file)
3. Hand off to gitea-prs to open a PR from "feat/add-example" into "main".
new_branch_name on create_or_update_file replaces a separate branch-creation call — the branch is created and the commit lands on it in one step.
Update a file when you don't already have its SHA
SHA is mandatory for updates. If it wasn't captured earlier in the conversation:
1. get_file_contents
owner, repo
ref: "main"
path: "docs/example.md"
→ read the top-level `sha` field (not content.sha)
2. create_or_update_file
owner, repo
path: "docs/example.md"
content: "<new base64-encoded content>"
message: "docs: update example"
branch_name: "main"
sha: "<sha from step 1>"
Do not guess or omit the SHA — the write either fails (409 on create-path fallback) or is rejected outright.
Delete a file
Same SHA-first pattern, no fallback path:
1. get_file_contents owner, repo, ref: "main", path: "docs/old-example.md"
→ read the top-level `sha` field
2. delete_file
owner, repo
path: "docs/old-example.md"
message: "docs: remove old example"
branch_name: "main"
sha: "<sha from step 1>"