docs(adr): ADR 0064 — deprecate customized/ directory overlay

Signed-off-by: Greg Allen <gallen@redhat.com>
Signed-off-by: Claude Opus 4.6 <noreply@anthropic.com>
Signed-off-by: Greg Allen <gallen@redhat.com>

Author: ggallen

docs/ADRs/0035-layered-content-resolution.md

@@ -1,6 +1,6 @@
 ---
 title: "35. Layered content resolution"
-status: Accepted
+status: Superseded
 relates_to:
   - agent-infrastructure
   - agent-architecture
@@ -17,7 +17,7 @@ Date: 2026-05-09
 
 ## Status
 
-Accepted
+Superseded by [ADR 0064](0064-deprecate-customized-directory-overlay.md).
 
 ## Context
 

docs/ADRs/0064-deprecate-customized-directory-overlay.md

@@ -0,0 +1,101 @@
+---
+title: "64. Deprecate customized/ directory overlay"
+status: Accepted
+relates_to:
+  - agent-infrastructure
+  - agent-architecture
+topics:
+  - layering
+  - customization
+  - deprecation
+---
+
+# 64. Deprecate customized/ directory overlay
+
+Date: 2026-06-30
+
+## Status
+
+Accepted
+
+Supersedes [ADR 0035](0035-layered-content-resolution.md) (layered content
+resolution).
+
+## Context
+
+[ADR 0035](0035-layered-content-resolution.md) introduced a three-tier
+layering model for agent customization: upstream defaults are copied into the
+workspace at runtime, then files from `customized/` (per-org) or
+`.fullsend/customized/` (per-repo) are overlaid on top, replacing upstream
+files with matching names. The overlay is file-level replacement with no
+field-level merging — customizing a single harness field requires copying the
+entire upstream YAML and modifying it.
+
+Three subsequent ADRs have introduced mechanisms that cover every
+customization scenario the overlay handled, with better ergonomics:
+
+- [ADR 0045](0045-forge-portable-harness-schema.md) added `base:`
+  composition for harness files. A thin wrapper inherits an upstream harness
+  by URL and overrides only the fields that differ, with proper merge
+  semantics (scalars override, skills concatenate, runner_env merges).
+
+- [ADR 0038](0038-universal-harness-access.md) added URL-based references
+  for declarative resources (agents, skills, policies, schemas). Resources
+  can be referenced from any trusted source without copying them into a
+  local directory.
+
+- [ADR 0058](0058-agent-registration.md) added config-based agent
+  registration. Agents are discovered from `agents:` entries in config
+  (URLs or local paths), not from directory scanning.
+
+Together these make the `customized/` directory overlay redundant:
+
+| What `customized/` did | Replacement |
+|---|---|
+| Override a harness | `base:` composition (ADR 0045) |
+| Override an agent definition | Harness `agent:` field with path or URL (ADR 0038) |
+| Add/remove agents | `agents:` list in config (ADR 0058) |
+| Add custom skills | Harness `skills:` list with paths or URLs (ADR 0038); concatenated via `base:` (ADR 0045) |
+| Override policies/schemas | Harness fields with paths or URLs (ADR 0038) |
+| Custom scripts | `pre_script`/`post_script` in harness; inherited from `base:` (ADR 0045) |
+| Custom env vars | `env:` in harness; merged via `base:` (ADR 0045) |
+| Data files in `scripts/` (e.g. `.pre-commit-tools.yaml`) | L2 additive merge at repo root ([ADR 0056](0056-per-repo-precommit-tools-registry.md)); `base:` composition for harness-level overrides |
+
+**Scripts and env constraint:**
+[ADR 0038](0038-universal-harness-access.md) prohibits standalone URL
+references for executable resources. All script customization must go
+through `base:` harness composition (where scripts declared in the base
+are fetched from the same origin). The L1 full-replacement path for
+data files like `.pre-commit-tools.yaml` via `customized/scripts/`
+([ADR 0056](0056-per-repo-precommit-tools-registry.md)) is replaced by
+the L2 additive merge at repo root, which already covers per-repo
+customization without the overlay.
+
+The `customized/` directories currently contain only `.gitkeep` placeholders.
+The overlay loop in reusable workflows runs every agent invocation but copies
+zero files.
+
+## Decision
+
+Deprecate and remove the `customized/` directory overlay mechanism introduced
+by ADR 0035.
+
+The implementation plan is in
+[docs/plans/deprecate-customized-directory-overlay.md](../plans/deprecate-customized-directory-overlay.md).
+
+This ADR should be implemented once ADRs 0038, 0045, and 0058 are fully
+implemented and in production.
+
+## Consequences
+
+- Users who placed files in `customized/` must migrate to `base:`
+  composition, URL references, or config-based registration.
+- Deprecation warnings during install and updated documentation will guide
+  migration.
+- The reusable workflows become simpler — no overlay loop, no
+  `install_mode` branching for customization paths.
+- The scaffold produces fewer files — no `.gitkeep` placeholders in
+  `customized/` subdirectories.
+- `fullsend admin install` no longer creates `customized/` directories.
+- A single, consistent customization model replaces the split between
+  directory overlay (ADR 0035) and harness composition (ADR 0045).

docs/architecture.md

@@ -386,7 +386,10 @@ See [ADR 0003](ADRs/0003-org-config-repo-convention.md) for the config repo conv
   [ADR 0047](ADRs/0047-vendored-installs-with-vendor-flag.md)). The
   scaffold installs only org-specific files and a `customized/` directory for org
   overrides. Org files in `customized/` overwrite upstream defaults at runtime
-  ([ADR 0035](ADRs/0035-layered-content-resolution.md)).
+  ([ADR 0035](ADRs/0035-layered-content-resolution.md)). The `customized/`
+  overlay is deprecated; `base:` harness composition, URL resource
+  references, and config-based agent registration now cover all customization
+  scenarios ([ADR 0064](ADRs/0064-deprecate-customized-directory-overlay.md)).
 
 ## Multi-org deployment model