per-agent knowledgebases are not initialized in new TUI

### Checks

- [x] I have searched [github.com/aws/amazon-q-developer-cli/issues](https://github.com/aws/amazon-q-developer-cli/issues?q=) and there are no duplicates of my issue
- [x] I have run `q doctor` in the affected terminal session
- [x] 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

```yaml

[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"
```