The previous round taught agent-audit's validator to permit disallowedTools but left the skill that writes agents still forbidding it, in six places. Running agent-author on any of the three fenced orchestrators would have stripped the fence, and nothing would have caught it: the validator's allowlist is a permit list, so an absent field passes. The template was the worst of them, since its comment is copied verbatim into every new plugin-scope agent. Where a list had to be restated it is now a pointer to field-inventory.md's apm-agent-allowlist instead -- the same data validate.sh reads -- because a roster copied into a template goes stale one step further out than the roster itself. Where the text has to teach something it teaches the shape rule rather than the exception: tools is an allowlist whose vocabulary differs per harness, so verbatim copy makes one value wrong on one target; disallowedTools is a denylist, where an unrecognised name denies nothing, so the worst case is a missing fence rather than a wrongly granted capability. ADR-0016's amendment claimed an unrecognised key is inert on Copilot while the same ADR's Context says that behaviour is unconfirmed by research -- asserting as settled the exact thing it flags as unknown, and justifying it with apm's compile-time behaviour, which says nothing about Copilot's runtime. It is rewritten into labelled tiers: confirmed for Claude Code with citations, inferred by analogy for Copilot with the analogy's limits stated, unverified where it is unverified, and the residual risk accepted explicitly with its blast radius. It also no longer claims to restore a write sandbox: the denylist does not deny Bash, which these agents inherit and legitimately need. docs/hooks.md called the old root hooks.json a stale sync artifact -- it was added in the plugin's creating commit and pointed at by main's Copilot manifest -- and claimed both ecosystems now resolve hooks/hooks.json. Copilot does not: its hooks field has no default and no compiled manifest declares one, so it resolves nothing. Recorded as the gap it is, with re-injection noted as a follow-up rather than asserted away. Its event list is marked partial. Also: new-agent.bats asserted a hardcoded four-field allowlist and would have rejected a scaffolded agent carrying the field the ADR now blesses; it reads field-inventory.md too. And ADR-0016's premise that Claude's tools: is space-separated was wrong -- it takes a comma-separated string or a YAML list. The incompatibility with Copilot is the vocabulary, not the punctuation. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01X7GvKuJfy2WrdBmUttV4DT
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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 the fields in the apm-agent-allowlist section of agent-audit's references/field-inventory.md. That section is the authoritative list — agent-audit's validate.sh reads it from there as data, and it changes — so consult it rather than any restatement of it. apm compile copies this frontmatter verbatim to both the Claude Code and Copilot CLI compile targets with no per-target integrator, so a harness-specific value is guaranteed wrong on at least one target (ADR-0016).
The rule is about a field's shape, not a fixed roster. tools is an allowlist whose vocabulary differs per harness — Claude Code names its own tools, Copilot CLI uses aliases (execute/read/edit/search/agent/web) — so under verbatim copy one value is wrong on one target. It stays out. disallowedTools is a denylist, and denying by name has no such conflict: a name the other harness does not recognise denies nothing, so the worst case is that the fence is absent there, never that a capability is wrongly granted. That asymmetry is why the denylist is admitted where the allowlist is not (ADR-0016's 2026-08-14 amendment). Claude Code honours it for plugin subagents — docs/research/docs/claude-code-plugins/agent-definition.md:99 names the three fields plugin agents silently ignore (hooks, mcpServers, permissionMode) and disallowedTools is not among them. It is a partial fence: it denies only the tools it names, not Bash, which a plugin-scope agent with no tools inherits — so state read-only intent in the body too.
This makes the old "silently ignored at plugin scope" framing moot for the excluded fields. It's not that hooks, mcpServers, permissionMode, tools, isolation, maxTurns, effort, memory, 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.