Preserve independent project host setups

Co-authored-by: Orca <help@stably.ai>

notes/project-first-host-model-change-inventory.md

@@ -493,12 +493,15 @@ Already partially landed:
   compatibility projection and persistence sync
 - project-host setup runtime capability advertisement, read fallback, and
   remote mutation gating for older runtime servers
+- persistence merge that preserves independently persisted project/setup rows
+  across load, repo updates, and repo reorders while refreshing repo-backed
+  compatibility rows from repos
 
 Not complete yet:
 
 - SSH clone streamed-progress parity and provisioning flows
-- independent project-host setup persistence beyond the repo-backed
-  compatibility records
+- first-class independent project-host setup creation/update/delete APIs beyond
+  the current repo-backed import/clone compatibility paths
 - bulk setup flows and setup for hosts that are not already known to the client
 - project settings split into global and host-specific ownership
 - host settings/capability UI aligned with project setup

notes/project-first-host-model-conversation.md

@@ -497,11 +497,14 @@ Already partially landed:
   compatibility projection and persistence sync
 - project-host setup runtime capability advertisement, read fallback, and
   remote mutation gating for older runtime servers
+- persistence merge that preserves independently persisted project/setup rows
+  across load, repo updates, and repo reorders while refreshing repo-backed
+  compatibility rows from repos
 
 Not complete yet:
 
-- independent project-host setup persistence beyond repo-backed compatibility
-  records
+- first-class independent project-host setup creation/update/delete APIs beyond
+  the current repo-backed import/clone compatibility paths
 - bulk setup flows and setup for hosts that are not already known to the client
 - SSH streamed clone progress parity
 - full project settings split into global and host-specific ownership
@@ -531,7 +534,7 @@ tests, and version-skew handling.
 
 The largest remaining areas are:
 
-1. independent `ProjectHostSetup` persistence
+1. independent `ProjectHostSetup` creation/update/delete APIs
 2. project-first creation/setup UI completion
 3. project and host settings ownership split
 4. cache/request ownership audit

notes/project-first-host-model-discussion.md

@@ -532,14 +532,17 @@ Already partially landed:
   compatibility projection and persistence sync
 - project-host setup runtime capability advertisement, read fallback, and
   remote mutation gating for older runtime servers
+- persistence merge that preserves independently persisted project/setup rows
+  across load, repo updates, and repo reorders while refreshing repo-backed
+  compatibility rows from repos
 
 Not complete yet:
 
 - SSH clone streamed-progress parity
 - provisioning flows and inline provisioning actions from the composer
 - bulk setup flows and setup for hosts that are not already known to the client
-- independent project-host setup persistence beyond repo-backed compatibility
-  records
+- first-class independent project-host setup creation/update/delete APIs beyond
+  the current repo-backed import/clone compatibility paths
 - full project settings split into global and host-specific ownership
 - host settings/capability UI aligned with project setup
 - complete cache/request ownership audit

notes/project-first-host-model-handoff.md

@@ -415,12 +415,15 @@ Already partially landed:
 - repo-backed setup method metadata for imported/cloned project-host setups
 - project-host setup runtime capability advertisement, read fallback, and
   remote mutation gating for older runtime servers
+- persistence merge that preserves independently persisted project/setup rows
+  across load, repo updates, and repo reorders while refreshing repo-backed
+  compatibility rows from repos
 
 Still needed:
 
 - finish SSH clone streamed-progress parity and provisioning flows
-- independent project-host setup persistence beyond the repo-backed
-  compatibility records
+- first-class independent project-host setup creation/update/delete APIs beyond
+  the current repo-backed import/clone compatibility paths
 - bulk setup flows and setup for newly added hosts
 - project settings split into global and host-specific ownership
 - host settings/capability UI aligned with project setup

notes/project-first-host-model.md

@@ -766,16 +766,20 @@ Landed so far:
   advertise `project-host-setup.v1`; new clients fall back to repo-derived
   project/setup projection for reads when that capability is missing and block
   remote setup/clone mutations before contacting an older server.
+- Added a persistence merge for project-host setup state. Repo-backed
+  compatibility rows are still refreshed from repos, but independently
+  persisted projects/setups now survive load, repo update, and repo reorder
+  paths instead of being overwritten by the repo projection.
 - Added tests for local repos, SSH repos, same-provider multi-host grouping,
   no-identity same-name non-grouping, selector cache behavior, persistence
   backfill, repo mutation synchronization, renderer hydration, runtime RPC
-  routing, project-host setup capability gating, setup method persistence,
-  local/runtime/SSH clone setup composition, remote clone IPC, and GitHub clone
-  URL inference. Sidebar row-builder tests now cover project-first multi-host
-  grouping and same-name repo separation without project identity. Workspace
-  target tests cover local-only fallback, focused-host setup selection, explicit
-  project-plus-host resolution, same-name non-merging, and unavailable setup
-  reasons.
+  routing, project-host setup capability gating, independent setup preservation,
+  setup method persistence, local/runtime/SSH clone setup composition, remote
+  clone IPC, and GitHub clone URL inference. Sidebar row-builder tests now cover
+  project-first multi-host grouping and same-name repo separation without
+  project identity. Workspace target tests cover local-only fallback,
+  focused-host setup selection, explicit project-plus-host resolution, same-name
+  non-merging, and unavailable setup reasons.
 
 Important limitation:
 
@@ -791,15 +795,19 @@ Important limitation:
   not yet have local-clone parity for progress events. Abort now propagates to
   the relay `git.exec` request, and failed/aborted SSH clones clean up only
   when Orca can prove the target did not already exist before the clone.
-- Project-host setup records are still regenerated from repo compatibility
-  records. The setup method now persists through that projection, but the final
-  independent setup table is still future work.
+- Repo-backed project-host setup records are still regenerated from repo
+  compatibility records. Independently persisted setup records are now preserved
+  across load and repo mutations, but the UI/API still mostly creates setups
+  through repo-backed import/clone paths. A fully independent setup creation and
+  mutation table is still future work.
 
 Remaining end-to-end work:
 
 - broaden setup-on-host flows beyond known local, SSH, and active runtime hosts
 - finish SSH clone streamed-progress parity, provisioning, and bulk setup-on-host
   flows
+- add first-class independent project-host setup creation/update/delete APIs
+  instead of routing most setup changes through repo import/update compatibility
 - split settings into explicit client, host, project, and project-host setup
   scopes
 - validate the default project-first sidebar view in Electron and continue