Cross-repository schema rename omits secondary-repository indexing warnings #1425

Problem

Cross-repository schema rename still does not collect indexing warnings from secondary repositories.

Original review: #392 (comment)

Current evidence

At main d9461c50c7aa778a5a400b53721fcd0d7296f312:

• tools/refactor_handlers/schema_codemod.rs:61–79 gathers repos and directly calls schema::rename_across; it does not recursively execute a tool per root.
• schema/across.rs:39 invokes rename for each root. schema/execute.rs:107 performs the LSP rename with that root.
• session/types.rs:79 records indexing notes under each session root.
• tools/inspection_handlers.rs:122 drains only the single root passed to with_indexing_notes; tools/execution.rs:367 passes the originating workspace root.
• No secondary-root drain is present in the schema path; its apply gate examines diagnostics, not the stored indexing notes.

Reproduce and expected

Use code_schema_rename with a secondary repo whose engine returns an indexing/loading warning for a rename query. The note is stored under the secondary repo, omitted from the current response, and may leak into a later unrelated call. Collect warnings for every root queried (or attach them directly to the request result), report incomplete evidence, and ensure write decisions do not silently treat it as complete. Include a secondary-root warning regression.

Verification

Source/call-site audit only; no cross-repository edits or fresh LSP/compiler test was executed.