diff --git a/projects.py b/projects.py
index a950d3f..9dd0d9c 100644
--- a/projects.py
+++ b/projects.py
@@ -8,9 +8,16 @@
 
 Two properties are deliberate:
 
-**Explicit config always wins.** ``github.repos`` set ⇒ the registry is not
-consulted at all. Same non-regression property the core work has: configuring
-nothing new keeps today's behavior byte for byte.
+**Explicit config is ADDED to, never replaced — and never hides the registry.**
+``github.repos`` set ⇒ those repos come FIRST, in the operator's order, and the
+registry's repos follow (deduped). v0.4.0 made an explicit list WIN outright, on the
+non-regression argument — but that turned "I typed a repos list once" into "the
+registry is dead for me forever": every project the agent onboarded afterwards
+(`onboard_project` registers into ``projects:``) stayed invisible to ``/issue`` and
+the board, silently, with no config knob to opt back in (2026-08-20, protoEngineer:
+three self-onboarded repos never reached the picker). A union is still
+non-regressing for everything the explicit list names (same entries, same order,
+same default) — it only adds the registry's entries after them.
 
 **Every read degrades to ``[]``.** The plugin's ``min_protoagent_version`` stays
 0.27.0 — the projection is additive, and bumping the floor would cut off older
@@ -25,27 +32,36 @@
 
 def registry_repos() -> list[str]:
     """``owner/name`` for every registered project that declares one — config
-    order, deduped, blanks dropped. ``[]`` on any host without the registry."""
+    order, deduped, blanks dropped. ``[]`` on any host without the registry.
+
+    Reads the ADR 0095 ``projects:`` registry first, then the legacy explicit
+    ``filesystem.projects`` override: an instance that predates the registry (or
+    one written by the pre-#2925 ``onboard_project``) carries its ``github``
+    bindings THERE, and those repos are just as real. Registry entries lead."""
     try:
         from graph.sdk import config
 
-        entries = getattr(config(), "projects", None) or []
+        cfg = config()
+        entries = list(getattr(cfg, "projects", None) or []) + list(getattr(cfg, "filesystem_projects", None) or [])
     except Exception:  # noqa: BLE001 — no host / older host / config unloaded; never fatal
         return []
+    return _dedupe(str(e.get("github") or "") for e in entries if isinstance(e, dict))
+
+
+def effective_repos(cfg_repos: list | None) -> list[str]:
+    """The repo picker list: the explicit ``github.repos`` entries (operator order,
+    first) UNION the host's managed-projects registry. The single place the two
+    layers meet — and the reason an onboarded project needs no second declaration."""
+    explicit = [str(r).strip() for r in (cfg_repos or []) if str(r).strip()]
+    return _dedupe([*explicit, *registry_repos()])
+
+
+def _dedupe(repos) -> list[str]:
     out: list[str] = []
     seen: set[str] = set()
-    for entry in entries:
-        if not isinstance(entry, dict):
-            continue
-        repo = str(entry.get("github") or "").strip()
+    for repo in repos:
+        repo = repo.strip()
         if repo and repo not in seen:
             seen.add(repo)
             out.append(repo)
     return out
-
-
-def effective_repos(cfg_repos: list | None) -> list[str]:
-    """The repo picker list: explicit ``github.repos`` when set, else the host's
-    managed-projects registry. The single place the two layers meet."""
-    explicit = [str(r).strip() for r in (cfg_repos or []) if str(r).strip()]
-    return explicit or registry_repos()
diff --git a/protoagent.plugin.yaml b/protoagent.plugin.yaml
index b1a1b53..1b2389d 100644
--- a/protoagent.plugin.yaml
+++ b/protoagent.plugin.yaml
@@ -2,7 +2,7 @@
 # Keep `version` in lockstep with pyproject.toml (tests/test_version.py asserts it).
 id: github
 name: GitHub (read/write tools)
-version: 0.4.0
+version: 0.5.0
 description: >-
   Read AND write GitHub tools over the `gh` CLI, with PER-AGENT write gating. The
   read tools (PRs, issues, diffs, CI, repo files/contents) are always on; the write
@@ -24,13 +24,15 @@ config:
   write: false                 # false = read tools only; true = read + write tools
   default_repo: ""             # preselected repo for /issue (owner/name); "" = none
   repos: []                    # repo picker list (each owner/name) for /issue + views.
-                               # LEAVE EMPTY to inherit the host's managed-projects
-                               # registry (ADR 0095, protoAgent 0.115.0+): every
-                               # `projects:` entry with a `github:` field feeds the
-                               # picker, so a project is declared once instead of here
-                               # as well. Setting this list explicitly WINS and the
-                               # registry is not consulted; on older hosts (or with no
-                               # registry configured) behavior is unchanged.
+                               # The host's managed-projects registry (ADR 0095,
+                               # protoAgent 0.115.0+) is ALWAYS added: every `projects:`
+                               # entry with a `github:` field (and any legacy
+                               # filesystem.projects entry carrying one) feeds the
+                               # picker, so a project — including one the agent
+                               # onboards itself — is declared once. Entries listed
+                               # here come first, in this order, so the default-repo
+                               # resolution is unchanged; the registry's follow.
+                               # Older hosts with no registry: behavior is unchanged.
 
 # Settings (ADR 0019) — surfaced as editable fields in the console.
 settings:
diff --git a/pyproject.toml b/pyproject.toml
index 67f63ae..137b162 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "github-plugin"
-version = "0.4.0"
+version = "0.5.0"
 description = "Read/write GitHub tools for protoAgent over the gh CLI, with per-agent write gating."
 requires-python = ">=3.11"
 
diff --git a/tests/test_projects.py b/tests/test_projects.py
index 6c44a27..8e91adc 100644
--- a/tests/test_projects.py
+++ b/tests/test_projects.py
@@ -20,13 +20,13 @@
 def fake_host(monkeypatch):
     """Install a fake `graph.sdk` whose config() returns the given projects list."""
 
-    def _install(projects, *, raises: bool = False):
+    def _install(projects, *, raises: bool = False, fence=None):
         sdk = types.ModuleType("graph.sdk")
 
         def config():
             if raises:
                 raise RuntimeError("config not loaded")
-            return types.SimpleNamespace(projects=projects)
+            return types.SimpleNamespace(projects=projects, filesystem_projects=fence)
 
         sdk.config = config
         graph = types.ModuleType("graph")
@@ -81,10 +81,29 @@ def test_registry_repos_are_deduped_in_config_order(fake_host):
     assert registry_repos() == ["o/a", "o/c"]
 
 
-def test_explicit_repos_win_over_the_registry(fake_host):
-    """Non-regression: a configured picker list means the registry is never consulted."""
-    fake_host([{"name": "a", "path": "/a", "github": "o/registry"}])
-    assert effective_repos(["o/explicit"]) == ["o/explicit"]
+def test_explicit_repos_lead_and_the_registry_follows(fake_host):
+    """An explicit picker list is ADDED TO by the registry, never replaced by it and
+    never allowed to hide it: the operator's entries keep their order (and so the
+    default-repo resolution), the registry's come after, deduped. v0.4.0's
+    explicit-wins made one typed list bury every later onboard_project forever."""
+    fake_host(
+        [{"name": "a", "path": "/a", "github": "o/registry"}, {"name": "b", "path": "/b", "github": "o/explicit"}]
+    )
+    assert effective_repos(["o/explicit", "o/other"]) == ["o/explicit", "o/other", "o/registry"]
+
+
+def test_registry_also_reads_github_bindings_on_the_legacy_fence_override(fake_host):
+    """A pre-registry instance (or one written by the pre-#2925 onboard tool) carries
+    `github:` on filesystem.projects entries — those repos count, after the registry's."""
+    fake_host(
+        [{"name": "a", "path": "/a", "github": "o/reg"}],
+        fence=[
+            {"name": "x", "path": "/x", "github": "o/fence"},
+            {"name": "y", "path": "/y"},
+            {"name": "z", "path": "/z", "github": "o/reg"},
+        ],
+    )
+    assert registry_repos() == ["o/reg", "o/fence"]
 
 
 def test_registry_fills_an_empty_picker(fake_host):
diff --git a/uv.lock b/uv.lock
index 460aaac..49d2ced 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4,5 +4,5 @@ requires-python = ">=3.11"
 
 [[package]]
 name = "github-plugin"
-version = "0.4.0"
+version = "0.5.0"
 source = { virtual = "." }