fix: updated execute_command to not mangle heredocs and also added explicit instructions to the coder and sisyphus agents to use fs_write and fs_patch over execute_command when writing files

assets/agents/coder/graph.yaml

@@ -177,8 +177,14 @@ nodes:
 
       1. Use `fs_patch` for surgical edits to existing files.
       2. Use `fs_write` for new files or full rewrites.
-      3. NEVER output code to chat. Always use tools.
+      3. NEVER write files via `execute_command`. Do not use `cat >`,
-      4. ALWAYS pass ABSOLUTE paths to fs_write and fs_patch. Relative
+         `cat >>`, `echo >`, `printf >`, `tee`, heredocs (`<<EOF`), or
+         `python3 -c "open(...).write(...)"`. Shell-based file writes
+         break on multi-line content, special characters, quoted strings,
+         and nested language blocks. `fs_write` and `fs_patch` handle
+         these correctly because they don't go through shell parsing.
+      4. NEVER output code to chat. Always use tools.
+      5. ALWAYS pass ABSOLUTE paths to fs_write and fs_patch. Relative
          paths resolve against the coyote invocation directory (not the
          project dir), which is rarely what you want. The project root
          is {{project_dir}}.

assets/agents/sisyphus/config.yaml

@@ -39,6 +39,8 @@ global_tools:
   - fs_grep.sh
   - fs_glob.sh
   - fs_ls.sh
+  - fs_write.sh
+  - fs_patch.sh
   - execute_command.sh
 
 instructions: |
@@ -237,6 +239,24 @@ instructions: |
 
   **No evidence = not complete.** Mark a todo `completed` only after evidence is collected.
 
+  ## File Operations (Direct Edits)
+
+  When you write or modify files yourself (rather than delegating to coder):
+
+  - **For writing files**, ALWAYS use `fs_write` (new file / full overwrite) or `fs_patch` (surgical edit). NEVER write files via `execute_command`. Do not use:
+    - `cat > file`, `cat >> file`, `tee`
+    - `echo >`, `printf >`
+    - Heredocs (`<<EOF`, `<<-EOF`, `<<'EOF'`)
+    - `python3 -c "open(...).write(...)"` or similar one-liners in any language
+    - Any other shell-based file write mechanism
+
+    Shell-based file writes break on multi-line content, special characters, quoted strings, and nested language blocks (Python triple-strings, JSON, etc.). `fs_write` and `fs_patch` handle these correctly because they don't go through shell parsing.
+
+  - **For reading files**, prefer `fs_read` over `cat` via `execute_command`. `fs_read` supports offset/limit for partial reads.
+  - **For listing/searching**, prefer `fs_ls`, `fs_glob`, `fs_grep` over shell equivalents (`ls`, `find`, `grep`).
+
+  `execute_command` is for: git operations, build/test commands, package management, runtime inspection (`ps`, `df`, etc.) — anything where the shell IS the right interface.
+
   ## Phase 7 - Failure Recovery
 
   ### 3-strike rule
@@ -307,6 +327,7 @@ instructions: |
   - Marking todos complete without evidence → dishonest reporting
   - Suppressing errors (`as any`, `@ts-ignore`, `#[allow(...)]`, empty catches) → hidden bugs
   - 3 fix attempts without consulting Oracle → wasted budget
+  - Writing files via `execute_command` (heredocs, `cat >`, `echo >`, `printf >`) → file corruption from shell parsing
 
   ## Hard Blocks (NEVER violate)
 
@@ -315,6 +336,7 @@ instructions: |
   - Speculate about unread code → never
   - Leave code in broken state after failures → never
   - Deliver final user answer with Oracle still running → never
+  - Write files via `execute_command` instead of `fs_write`/`fs_patch` → never
 
   ## Available Tools
   {{__tools__}}

assets/functions/tools/execute_command.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -e
 
-# @describe Execute the shell command.
+# @describe Execute the shell command. DO NOT use this to write files — use fs_write (new files) or fs_patch (edits) instead. Shell-based file writes (cat >, echo >, printf >, tee, heredocs, python -c "open(...)") break on multi-line content, special characters, quoted strings, and nested language blocks.
 # @option --command! The command to execute.
 
 # @env LLM_OUTPUT=/dev/stdout The output path
@@ -11,6 +11,11 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 main() {
     guard_operation
+    local script
+    script="$(mktemp)"
+    # shellcheck disable=SC2064
+    trap "rm -f '$script'" EXIT
     # shellcheck disable=SC2154
-    eval "$argc_command" >> "$LLM_OUTPUT"
+    printf '%s\n' "$argc_command" > "$script"
+    bash "$script" >> "$LLM_OUTPUT"
 }