bug: Database resource leaks and stream reader not cancelled

[RobertLD]

Problem

Multiple CLI commands open database connections without guaranteed cleanup via finally blocks. Additionally, a stream reader in url-fetcher is not properly cancelled on errors.

Severity: Major

Affected Files

CLI database leaks (src/cli/index.ts)

Commands that call initializeApp() or initializeAppWithEmbedding() without wrapping in try-finally with closeDatabase():

Command	Approximate Line
pack remove	1312
pack list (installed path)	1334
pack create	1365
connect obsidian	1545
disconnect obsidian	1727
disconnect notion	1795

Stream reader leak (src/core/url-fetcher.ts)

File	Lines	Issue
src/core/url-fetcher.ts	117-148	reader from response.body.getReader() not cancelled in finally block — only cancelled on size limit exceeded

Implementation Plan

1. Add try-finally to all CLI commands

For each affected command, wrap the body in try-finally:

const { db } = initializeApp();
try {
  // existing command body
} finally {
  closeDatabase();
}

2. Fix stream reader cleanup

url-fetcher.ts lines 117-148: Wrap reader usage in try-finally:

const reader = response.body.getReader();
try {
  let result = await reader.read();
  while (!result.done) {
    totalBytes += result.value.byteLength;
    chunks.push(result.value);
    if (totalBytes > maxBytes) {
      break;  // reader.cancel() handled in finally
    }
    result = await reader.read();
  }
} finally {
  await reader.cancel();
}

3. Tests

• Verify closeDatabase is called on command error paths (check with mock)
• Test url-fetcher reader cancellation on error