fix: address PR #504 review warnings

- workspace-context: a transiently unavailable but still-effective candidate
  keeps its cached trimmed digest in the directory's dedup slot, so an
  identical later sibling is not emitted as a duplicate set until the next
  successful reconciliation
- app-boot: --resume rejects a following token that is itself resume syntax
  instead of accepting it as a session id
- tui: the queued-steering badge tracks per-entry sources and a drain removes
  one matching entry, so loop-authored steering (no agent/queued) cannot
  consume a pending user message's slot

packages/context/workspace-context/src/state.ts

@@ -448,7 +448,17 @@ export async function reconcileInstructionContext(
     const { directory } = decodeScopeKey(scope)
     const previous = effective.get(scope)
     const probe = await probeScopeInstruction(scope, projectRoot, resolved, fileSystem, options.signal)
-    if (probe.kind === 'unavailable') continue
+    if (probe.kind === 'unavailable') {
+      // Last-good-state: the candidate stays effective, so its cached trimmed
+      // digest must keep occupying the directory's dedup slot — otherwise an
+      // identical later sibling would be emitted as a duplicate `set` until the
+      // next successful reconciliation removed it again.
+      const cached = versions.get(scope)
+      if (cached !== undefined && previous !== undefined && previous.action !== 'remove') {
+        registerKeptTrimmed(directory, cached.trimmedDigest)
+      }
+      continue
+    }
     if (probe.kind === 'absent') {
       if (previous === undefined || previous.action === 'remove') versions.delete(scope)
       else pushRemoval(scope, previous.path)

packages/context/workspace-context/tests/workspace-context.spec.ts

@@ -2201,6 +2201,47 @@ describe('dynamic nested workspace context injection', () => {
     }
   })
 
+  it('keeps deduplicating against a loaded candidate whose probe transiently fails', async () => {
+    const root = await tempRepo()
+    const home = await tempRepo()
+    const ctx = new Context()
+    try {
+      await ctx.plugin(SystemPrompt)
+      await ctx.plugin(ToolRegistry)
+      await ctx.plugin(RecordingFileSystem)
+      const fs = ctx.fs as RecordingFileSystem
+      fs.entries.set(join(root, '.git'), { type: 'directory' })
+      fs.entries.set(join(root, 'pkg/AGENTS.md'), { type: 'file', content: 'nested rule' })
+      fs.entries.set(join(root, 'pkg/file.txt'), { type: 'file', content: 'hello' })
+      await ctx.plugin(ToolFs)
+      await ctx.plugin(workspaceContext, { dshHome: home, maxBytes: 65536 })
+      const agent = stubAgent(root)
+
+      const first = await ctx.tools.execute({
+        signal: testToolSignal,
+        callId: CallId('read-before-transient-probe-failure'), name: 'read', arguments: { file_path: join('pkg', 'file.txt') }, agent,
+      })
+      appendAdditionalContexts(agent, first)
+      expect(first.additionalContexts).toBeDefined()
+
+      // The loaded candidate's probe fails while an identical sibling appears:
+      // the cached candidate stays effective (last good state), so the sibling
+      // must still deduplicate against it rather than land as a duplicate set.
+      fs.throwOnStat.add(join(root, 'pkg/AGENTS.md'))
+      fs.entries.set(join(root, 'pkg/CLAUDE.md'), { type: 'file', content: 'nested rule' })
+      const duringFailure = await ctx.tools.execute({
+        signal: testToolSignal,
+        callId: CallId('read-during-transient-probe-failure'), name: 'read', arguments: { file_path: join('pkg', 'file.txt') }, agent,
+      })
+
+      expect(duringFailure.additionalContexts).toBeUndefined()
+    } finally {
+      await ctx.fiber.dispose()
+      await rm(root, { recursive: true, force: true })
+      await rm(home, { recursive: true, force: true })
+    }
+  })
+
   it('removes a previously rendered sibling once its content becomes a duplicate of an earlier candidate', async () => {
     const root = await tempRepo()
     const home = await tempRepo()