per-agent knowledgebases are not initialized in new TUI

[justin8]

Checks

• I have searched github.com/aws/amazon-q-developer-cli/issues and there are no duplicates of my issue
• I have run q doctor in the affected terminal session
• I have run q restart and replicated the issue again

Operating system

macOS 26.3.1 (25D2128)

Expected behaviour

When knowledgebases are added in an agent's resources block they work as expected on the legacy UI:

• If they don't exist, they get created
• They're accessible consistently in the agent as defined in the config

Actual behaviour

Currently they are NOT created if they do not already exist when the agent is invoked using the new TUI. If the agent has been run using the legacy UI, it will create the knowledgebases there and they continue to exist when opened in the TUI. However if the TUI is used exclusively they never get initialized.

Steps to reproduce

1. Create an agent with a knowledgebase:

{
  "resources": [
    {
      "indexType": "best",
      "autoUpdate": true,
      "name": "MyFirstKnowledgebase",
      "description": "Super useful description",
      "source": "file:///path/to/kb",
      "type": "knowledgeBase"

2. Open the agent in the TUI: kiro-cli --agent my-agent --tui
3. Check with /knowledge show and see no knowledgebases
4. Restart with kiro-cli --agent my-agent --legacy-ui
5. Check with /knowledge show and see there are now knowledgebase(s)
6. Restart with TUI again, and running /knowledge show will now list the knowledgebases

Environment

<This will be visible to anyone. Do not include personal or sensitive information>

[q-details]
version = "2.1.1"
hash = "1d2ba18834ea4e6a88312b0dc70b2014b703aa6e"
date = "2026-04-25T00:22:45.193459Z (3d ago)"
variant = "full"

[system-info]
os = "macOS 26.3.1 (25D2128)"
chip = "Apple M3 Pro"
total-cores = 12
memory = "36.00 GB"

[environment]
cwd = "/Users/USER"
cli-path = "/Users/USER"
os = "Mac"
shell-path = "/Users/USER/.toolbox/tools/toolbox/1.1.4735.0/toolbox-exec"
shell-version = "5.9"
terminal = "iTerm 2"
install-method = "toolbox"

[env-vars]
PATH = "/Users/USER/.local/share/mise/installs/node/24.9.0/bin:/Users/USER/.local/share/mise/installs/python/3.13.7/bin:/Users/USER/.nix-profile/bin:/Users/USER/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/USER/go/bin:/Users/USER/.cargo/bin:/Users/USER/.toolbox/bin:/Users/USER/.yarn/bin:/Users/USER/.yadm-project:/Users/USER/.local/bin:/Users/USER/.local/gnubin:/Users/USER/.aim/mcp-servers:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/Applications/iTerm.app/Contents/Resources/utilities:/usr/local/sbin:/Users/USER/.rvm/bin"
QTERM_SESSION_ID = "ea520fcd841240a69387ce558c0521ee"
Q_SET_PARENT_CHECK = "1"
Q_TERM = "2.1.1"
SHELL = "/bin/zsh"
TERM = "xterm-256color"
ZDOTDIR = "/Users/USER"
__CFBundleIdentifier = "com.googlecode.iterm2"