Fix tool edge cases

[rizwan3d]

Summary

Fix several tool/runtime edge cases:

• allow empty file writes for truncation and placeholder files
• cap captured process output before it can grow unbounded in memory
• preserve final-newline changes in apply_patch updates
• write workspace files with explicit BOM-less UTF-8
• harden recursive workspace traversal against unreadable paths

The empty-response fallback/session-history issue was already fixed in the current branch baseline; this branch preserves that behavior.

Validation

• dotnet test NanoAgent.slnx from a clean temp copy: 274 passed, 0 failed