fix: S7735 — flip negated conditions (31 occurrences)

[RobertLD]

SonarCloud S7735 — Unexpected negated condition

31 occurrences of if (!condition) { A } else { B } that should be flipped to if (condition) { B } else { A } for readability.

Affected files:

• src/core/ — indexing.ts, packs.ts, search.ts, graph.ts
• src/cli/index.ts
• src/connectors/ — onenote.ts, obsidian.ts, notion.ts, confluence.ts, slack.ts
• src/registry/sync.ts
• src/mcp/server.ts
• Various test files

Fix: Mechanical — swap the if/else branches and remove the negation.

Severity: MINOR | Effort: ~30min mechanical