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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source_keys
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Agent Deployment Modes
Agent definitions deploy at three scopes and behave differently at each. The scope determines which fields are honoured, where files must live, and what identifiers users invoke.
Scope hierarchy and precedence
| Scope | Claude Code path | Copilot CLI path | Who it affects |
|---|---|---|---|
| User | ~/.claude/agents/ |
~/.copilot/agents/ |
All sessions for this user |
| Project | .claude/agents/ |
.github/agents/ or .copilot/agents/ |
This repo only |
| Plugin/APM | <package-root>/.apm/agents/<name>.agent.md — single vendor-neutral file, apm compile emits it to both targets |
(same file) | Sessions with the plugin/package installed |
When the same agent name appears at multiple scopes, user scope wins over project scope wins over plugin scope in Claude Code. In Copilot CLI, repo-level agents override enterprise and org-level; home-directory (user) agents override repo-level on name collision.
Plugin scope restrictions
Plugin/APM agents (.apm/agents/<name>.agent.md) carry only name, description, optionally model, and optionally source_keys (provenance metadata, not a runtime field — silently ignored by both harnesses) in frontmatter — full stop (see ADR-0016). apm compile copies this frontmatter verbatim to both the Claude Code and Copilot CLI compile targets with no per-target integrator: Claude's tools: (space-separated string) and Copilot's tools: (alias list) are incompatible vocabularies, and Claude-only fields have no Copilot equivalent, so any harness-specific value is guaranteed wrong on at least one target.
This makes the old "silently ignored at plugin scope" framing moot. It's not that hooks, mcpServers, permissionMode, tools, isolation, maxTurns, effort, memory, disallowedTools, skills, color, initialPrompt, or background are merely ignored at this scope — they are never written to the file at all. Copy the agent to .claude/agents/ (project scope) or ~/.claude/agents/ (user scope) to use any of them.
Scoped identifiers (Claude Code plugin agents only)
Plugin agents in subdirectories get compound identifiers:
plugins/my-plugin/.apm/agents/review/security.agent.md → my-plugin:review:security
Users must invoke with @agent-my-plugin:review:security. Keep agents flat in agents/ to avoid this — subdirectory nesting is rarely worth the UX cost.
At project and user scope, subdirectory path does not affect the agent's name.
Cache isolation
When a plugin is installed, its directory is copied to a cache. Any path that leaves the agent's plugin directory breaks post-install. Agent definition files must be self-contained — they cannot reference scripts, templates, or shared files outside the plugin.
Agents at project or user scope are read directly from disk; cache isolation does not apply.
Copilot CLI path conventions
| Scope | Expected path | Notes |
|---|---|---|
| User | ~/.copilot/agents/<name>.agent.md |
Home directory |
| Project | .github/agents/<name>.agent.md |
Standard; also .copilot/agents/ |
| Plugin/APM | <package-root>/.apm/agents/<name>.agent.md |
Not a Copilot-only file — this is the single vendor-neutral source apm compile reads for the Copilot CLI target |
The .agent.md extension is mandatory for real Copilot CLI files (project/user scope) — Copilot CLI does not pick up plain .md files in the agents/ directory. The plugin/APM source file also uses .agent.md by convention, since it compiles to Copilot CLI too, but it is not itself a Copilot file.