From 4f57d7116d9f497b9ebf5b9e378f0bbec136567f Mon Sep 17 00:00:00 2001
From: teknium1 <teknium1@gmail.com>
Date: Thu, 19 Feb 2026 09:24:04 -0800
Subject: [PATCH] Improved stdout handling in the terminal tool to prevent
 deadlocks by implementing a background thread to continuously drain output,
 ensuring smooth command execution without blocking.

---
 TODO.md                | 11 +++++++++++
 tools/terminal_tool.py | 37 ++++++++++++++++++++++++++++++-------
 2 files changed, 41 insertions(+), 7 deletions(-)

diff --git a/TODO.md b/TODO.md
index 8cee076e..0146734c 100644
--- a/TODO.md
+++ b/TODO.md
@@ -377,6 +377,17 @@ Both default to `false` in batch_runner and RL environments (checked programmati
 
 The bounded memory is the curated layer. For unbounded "long-term memory" -- searching past session transcripts -- see SQLite State Store (#5). A separate `session_search` tool provides ripgrep-style search over the full session history. This is never injected into the system prompt; the agent searches it on demand.
 
+### Known bug: duplicate entries are irrecoverable
+
+If the same content gets added twice (e.g., agent retries after a failed response generation and re-saves a memory it already saved), both `replace` and `remove` fail with "Multiple entries matched" because content-based matching can't disambiguate identical entries. The user/agent has no way to fix this without manually editing the file.
+
+**Possible fixes (pick one or combine):**
+- **Prevent on add**: reject or silently deduplicate when `content` exactly matches an existing entry. Cheapest fix, prevents the problem entirely.
+- **Remove-all flag**: `remove(target, old_text, remove_all=True)` deletes every match. Lets the agent nuke all copies, then re-add one if needed.
+- **Index-based fallback**: when multiple matches are found, return them with indices and accept `index` parameter on retry. More complex, but most precise.
+
+Simplest path: deduplicate on add (check before appending). One-line fix in `memory_tool.py`.
+
 ### Later (optional)
 - Periodic consolidation via cronjob/subagent: reviews recent session summaries, suggests memory updates. Needs subagents (#1).
 - Memory import/export: `hermes memory export` / `hermes memory import` for backup/migration.
diff --git a/tools/terminal_tool.py b/tools/terminal_tool.py
index da2d483d..ae379228 100644
--- a/tools/terminal_tool.py
+++ b/tools/terminal_tool.py
@@ -642,6 +642,11 @@ class _LocalEnvironment:
         Uses Popen + polling so the global interrupt event can kill the
         process early when the user sends a new message, instead of
         blocking for the full timeout.
+        
+        A background reader thread drains stdout continuously to prevent
+        pipe buffer deadlocks. Without this, commands producing >64KB of
+        output would block (Linux pipe buffer = 64KB) while the poll loop
+        waits for the process to finish — a classic deadlock.
         """
         work_dir = cwd or self.cwd or os.getcwd()
         effective_timeout = timeout or self.timeout
@@ -665,6 +670,25 @@ class _LocalEnvironment:
                 preexec_fn=os.setsid,
             )
             
+            # Drain stdout in a background thread to prevent pipe buffer
+            # deadlocks. The OS pipe buffer is 64KB on Linux; if the child
+            # writes more than that before anyone reads, it blocks forever.
+            _output_chunks: list[str] = []
+            def _drain_stdout():
+                try:
+                    for line in proc.stdout:
+                        _output_chunks.append(line)
+                except ValueError:
+                    pass  # stdout closed during interrupt/timeout
+                finally:
+                    try:
+                        proc.stdout.close()
+                    except Exception:
+                        pass
+            
+            reader = threading.Thread(target=_drain_stdout, daemon=True)
+            reader.start()
+            
             deadline = time.monotonic() + effective_timeout
             
             # Poll every 200ms so we notice interrupts quickly
@@ -676,9 +700,8 @@ class _LocalEnvironment:
                         os.killpg(os.getpgid(proc.pid), signal.SIGTERM)
                     except (ProcessLookupError, PermissionError):
                         proc.kill()
-                    # Grab any partial output
-                    partial, _ = proc.communicate(timeout=2)
-                    output = partial or ""
+                    reader.join(timeout=2)
+                    output = "".join(_output_chunks)
                     return {
                         "output": output + "\n[Command interrupted — user sent a new message]",
                         "returncode": 130  # Standard interrupted exit code
@@ -690,15 +713,15 @@ class _LocalEnvironment:
                         os.killpg(os.getpgid(proc.pid), signal.SIGTERM)
                     except (ProcessLookupError, PermissionError):
                         proc.kill()
-                    proc.communicate(timeout=2)
+                    reader.join(timeout=2)
                     return {"output": f"Command timed out after {effective_timeout}s", "returncode": 124}
                 
                 # Short sleep to avoid busy-waiting
                 time.sleep(0.2)
             
-            # Process finished normally — read all output
-            stdout, _ = proc.communicate()
-            return {"output": stdout or "", "returncode": proc.returncode}
+            # Process finished — wait for reader to drain remaining output
+            reader.join(timeout=5)
+            return {"output": "".join(_output_chunks), "returncode": proc.returncode}
             
         except Exception as e:
             return {"output": f"Execution error: {str(e)}", "returncode": 1}