docs: update bug tracking with Issue 2 fix completion

Both issues are now fixed and pushed:
- Issue 1: Follow mode respects --tail flag (7361e9d)
- Issue 2: Parser handles zap logger format (e958989)

Author: technicalpickles

docs/plans/2025-11-21-logs-command-bugs.md

@@ -342,15 +342,15 @@ cat ~/Library/Logs/mcpproxy/server-time.log | head -20
 - Deduplication continues to work correctly
 - Committed in commit 7361e9d
 
-### Issue 2: Investigation First (Before Fix)
+### Issue 2: Investigation and Fix (Completed)
 - [x] Examine raw log files from multiple servers
 - [x] Check log format consistency across servers
-- [ ] Review `internal/logs/logger.go` for timestamp writing
-- [ ] Check if Docker isolation affects log formatting
-- [ ] Check if upstream servers add their own timestamps
+- [x] Review `internal/logs/logger.go` for timestamp writing
+- [x] Check if Docker isolation affects log formatting
+- [x] Check if upstream servers add their own timestamps
 - [x] Determine root cause (A, B, or C from above) - **ROOT CAUSE: Scenario B - Parse Failure**
-- [ ] Implement appropriate fix based on findings
-- [ ] Test with multiple server types (HTTP, stdio, Docker-isolated)
+- [x] Implement appropriate fix based on findings
+- [x] Test with multiple server types (HTTP, stdio, Docker-isolated)
 
 **Investigation Results (2025-11-21)**:
 
@@ -381,7 +381,17 @@ Root cause confirmed as **Scenario B: Parse Failure with `time.Now()` Fallback**
 CLI added (time.Now)      Original from log file
 ```
 
-**Fix needed:** Update `parseLogLine()` to handle the actual log format produced by zap logger with pipe separators and ISO8601 timestamps.
+**Fix implemented (commit e958989):**
+- Updated `parseLogLine()` in `internal/server/server.go` to handle zap logger format
+- Parses ISO8601 timestamps using RFC3339 format
+- Strips file:line and JSON metadata from message display
+- Maintains backward compatibility with legacy format
+- Results in clean CLI output without double timestamps
+
+**After fix:**
+```
+2025-11-21T15:05:42.725-05:00 | INFO | MCP initialization completed successfully
+```
 
 ### Documentation
 - [ ] Update `docs/cli-management-commands.md` with correct `--tail` behavior