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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topic, source_keys
| topic | source_keys | |
|---|---|---|
| submodules |
|
Submodules — Deep Reference
Update flag reference
| Flag | Meaning |
|---|---|
--init |
Run init first (avoids a separate step) |
--remote |
Use the submodule's remote branch tip instead of the superproject's recorded commit |
--checkout |
Detached HEAD at recorded commit (default) |
--rebase |
Rebase current branch onto recorded commit |
--merge |
Merge recorded commit into current branch |
--recursive |
Operate on nested submodules |
--jobs <n> |
Parallel clone (defaults to submodule.fetchJobs) |
-N / --no-fetch |
Skip remote fetch |
--depth <n> |
Shallow clone |
--filter <spec> |
Partial clone filter |
Workflow patterns
Clone a repo with submodules
git clone --recurse-submodules <url> # Git 2.13+, one step
# or
git clone <url>
git submodule update --init --recursive
Add a dependency as a submodule
git submodule add https://github.com/org/lib.git libs/lib
git commit -m "chore: add lib as submodule"
Keep submodules pinned to the superproject's recorded commit
git submodule update --recursive # after every git pull
git config submodule.recurse true # do this automatically on pull
Update submodules to the latest commit on their tracked branch
git submodule update --remote --merge --recursive
git commit -am "chore: update submodules to latest"
Override a submodule URL locally (private mirror)
git submodule init
# edit .git/config: submodule.<name>.url = <mirror-url>
git submodule update
Local-only override (.git/config, not .gitmodules) — doesn't propagate to collaborators. Re-running sync overwrites it with the .gitmodules URL.
Removal, in full
deinit alone does not remove a submodule — it only clears .git/config and empties the working tree. To fully remove:
git submodule deinit -f <path> # unregister from .git/config
git rm <path> # remove .gitmodules entry + gitlink from index
rm -rf .git/modules/<name>/ # stale git dir; not tracked by git, not auto-cleaned
git commit -m "chore: remove <name> submodule"
.git/modules/<name>/ persisting after git rm will block re-adding the same path until manually deleted.
Relocate an embedded .git directory
git submodule absorbgitdirs [<path>...]
Moves a submodule's own .git directory into the superproject's .git/modules/<name>/, linking it back with a .git pointer file. Needed when a submodule was created or copied without going through git submodule add (e.g. converting a plain nested repo into a proper submodule).
foreach shell variables
Available inside the <command> argument to git submodule foreach:
| Variable | Meaning |
|---|---|
$name |
Logical submodule name |
$sm_path |
Path relative to superproject root |
$displaypath |
Path relative to current working directory |
$sha1 |
Recorded commit SHA |
$toplevel |
Superproject's root path |
git submodule foreach --recursive '<command>'
git submodule foreach 'git pull origin main || :' # || : continues past failures