Bug: Knowledge Base include/exclude patterns not applied during indexing (v1.27.3)

[isune-coder]

Bug Description

Both include_patterns and exclude_patterns from agent config and global settings are ignored during KB indexing. The resulting contexts.json always shows empty arrays, causing all files to be indexed.

Steps to Reproduce

1. Set knowledge.defaultExcludePatterns in ~/.kiro/settings/cli.json:

"knowledge.defaultExcludePatterns": [".obsidian/**", "Attachments/**"]

2. Set include in agent knowledgeBase resource config (~/.kiro/agents/sa-agent.json):

{
  "type": "knowledgeBase",
  "source": "file:///path/to/vault/",
  "include": ["**/*.md"],
  "autoUpdate": true
}

3. Start chat session, KB auto-indexes
4. Check ~/Library/Application Support/kiro-cli/knowledge_bases/*/contexts.json
5. Observe include_patterns: [] and exclude_patterns: []

Expected Behavior

• Agent config include: ["**/*.md"] should limit indexing to .md files only
• Global knowledge.defaultExcludePatterns should exclude matching directories
• contexts.json should reflect these patterns

Actual Behavior

• contexts.json shows: "include_patterns": [], "exclude_patterns": []
• 478 unique files indexed (expected ~285 .md files)
• 187 files from .obsidian/ directory included (should be excluded)
• Non-.md files indexed: .ts(72), .json(40), .js(14), .css(12), .pdf(6), .sh(3), .mjs(2)

Environment

• Kiro CLI: v1.27.3
• OS: macOS
• Index type: best

Notes

This was working in a previous version. The regression likely occurred in a recent update where the pattern fields are no longer passed through to the indexing engine.

[github-actions]

🤖 Potential Duplicate Detected

This issue appears to be similar to:

• #5795: Bug: --no-interactive mode overwrites contexts.json, deleting persistent Knowledge Bases (85% similar)
• #4876: Kiro doesn't respect .kiroignore file, try to read every files in the workspace and run out of context-usage everytime (85% similar)

What happens next?

• ⏰ This issue will be automatically closed in 3 days
• 🏷️ If this is not a duplicate, you can prevent automatic closure by adding a comment or reacting with 👎 to this message.
• 💬 Comment on the original issue if you have additional information

Why is this marked as duplicate?
Both issues report problems with contexts.json file handling in Knowledge Base functionality - the new issue shows patterns not being saved to contexts.json, while #5795 reports contexts.json being overwritten and deleting persistent Knowledge Bases. Both involve the same core system (KB contexts.json management) with data persistence failures.

[isune-coder]

Update: As of Kiro CLI v1.27.3 (current), I can no longer reproduce this issue.

After re-indexing my KB today (329 .md files from an Obsidian vault), the indexing completed correctly with only .md files included. The .obsidian/ directory and non-.md files were properly excluded.

This may have been resolved in a recent patch. Given the duplicate label, it's possible the fix was applied via the original issue. Happy to close this if the team confirms.

[github-actions]

Thank you for your feedback! 🙏

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