Adding folder to knowledge fails with incorrect file count

### 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 15.6.0 (24G84)

### Expected behaviour

When adding a folder to my knowledge base, I expect it to complete indexing successfully.

### Actual behaviour

When I add the root folder of my obsidian vault, I get an indexing error. The error says "Directory contains 5001 files, which exceeds the maximum limit of 5000 files"

I have confirmed there are 481 files using `find . -type f | wc -l`, so not even close to a 5000 file limit.

### Steps to reproduce

- Open q
- /knowledge add
- /knowledge status

### Environment

```yaml

[q-details]
version = "1.13.0"
hash = "7dee6efdf68f6343e80a56028e6b40f8eff77746"
date = "2025-07-31T02:57:26.581678Z (21h ago)"

[system-info]
os = "macOS 15.6.0 (24G84)"
chip = "Apple M3"
total-cores = 8
memory = "24.00 GB"

[environment]
cwd = "/Users/USER"
cli-path = "/Users/USER"
install-method = "unknown"

[env-vars]
PATH = "/Users/USER/Library/pnpm:/Users/USER/.local/share/bob/nvim-bin:/Users/USER/.cargo/bin:/Users/USER/.local/bin:/Users/USER/.toolbox/bin:/Users/USER/bin:/usr/local/bin:/Users/USER/.local/share/mise/installs/node/24.4.1/bin:/Users/USER/.local/share/mise/installs/python/3.12.7/bin:/Users/USER/.local/share/mise/installs/ruby/3.4.3/bin:/Users/USER/.local/share/mise/installs/usage/2.0.5:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/USER/.local/bin:/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:/Library/Apple/usr/bin:/Applications/Ghostty.app/Contents/MacOS:/Applications/Visual Studio Code.app/Contents/Resources/app/bin"
QTERM_SESSION_ID = "8b0790f5a8794f68860639e3eb1048a1"
Q_SET_PARENT_CHECK = "1"
Q_TERM = "1.13.0"
SHELL = "/bin/zsh"
TERM = "xterm-ghostty"
__CFBundleIdentifier = "com.mitchellh.ghostty"
```