fix(agents): align permissionMode acceptEdits across plugin and project layers (#732)

permissionMode: acceptEdits was declared only in the project copies of the documentation-writer and refactor-assistant write agents; the plugin copies omitted it, so the same write agents prompted on every edit in the standalone plugin distribution. Add the field to both plugin copies to align the layers, and document in CUSTOM_EXTENSIONS.md that permissionMode is kept identical across layers (it was previously missing from the intended-layer-diff list, making the gap a silent capability drift).

Author: kcenon

docs/CUSTOM_EXTENSIONS.md

@@ -210,7 +210,7 @@ pwsh scripts/sync_references.ps1   # Windows
 
 **Type**: Repository-internal convention
 
-The eight agent definitions exist in two layers — `project/.claude/agents/` and the standalone `plugin/agents/` bundle. They are near-duplicates but **not** byte-identical by design: frontmatter differs per layer (the project copy carries `color:`; neither carries the non-canonical `temperature:` field), and the body genericizes exactly one repo-specific "language-specific rules" sentence in the plugin copy.
+The eight agent definitions exist in two layers — `project/.claude/agents/` and the standalone `plugin/agents/` bundle. They are near-duplicates but **not** byte-identical by design: frontmatter differs per layer (the project copy carries `color:`; neither carries the non-canonical `temperature:` field; `permissionMode: acceptEdits` is kept identical across both layers for the two write agents, documentation-writer and refactor-assistant), and the body genericizes exactly one repo-specific "language-specific rules" sentence in the plugin copy.
 
 **CI enforcement**: `.github/workflows/validate-skills.yml` runs `scripts/check_agents.sh` (PowerShell twin: `scripts/check_agents.ps1`). It strips frontmatter and normalizes that single sentence, then fails (exit 2) if the agent **bodies** otherwise diverge — so a behavioral instruction edited in one layer but not the other cannot ship silently.
 

plugin/agents/documentation-writer.md

@@ -5,6 +5,7 @@ model: sonnet
 tools: Read, Write, Edit, Glob
 maxTurns: 30
 effort: high
+permissionMode: acceptEdits
 memory: project
 initialPrompt: "Check your memory for established documentation patterns and style conventions in this project."
 applies_to:

plugin/agents/refactor-assistant.md

@@ -5,6 +5,7 @@ model: sonnet
 tools: Read, Edit, Glob, Grep
 maxTurns: 25
 effort: high
+permissionMode: acceptEdits
 memory: project
 initialPrompt: "Check your memory for past refactoring decisions and established patterns in this project."
 applies_to: