fix: handle corrupted markers in remove, CRLF-safe end-marker consumption

1. Handle corrupted markers in remove_context_section() — mirror
   upsert's behavior: start-only removes start→EOF, end-only removes
   BOF→end. Previously bailed out leaving partial markers behind.

2. CRLF-safe end-marker consumption — both upsert and remove now
   handle \r\n after the end marker, not just \n. Prevents extra
   blank lines at replacement boundaries in CRLF files.

3. Clarify path rule in plan template — distinguish filesystem
   operations (absolute paths) from documentation/agent context
   references (project-relative paths).

Author: mnriem

src/specify_cli/integrations/base.py

@@ -492,6 +492,9 @@ def upsert_context_section(
             if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
                 # Replace existing section (include the end marker + newline)
                 end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                # Consume trailing line ending (CRLF or LF)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
                 if end_of_marker < len(content) and content[end_of_marker] == "\n":
                     end_of_marker += 1
                 new_content = content[:start_idx] + section + content[end_of_marker:]
@@ -501,6 +504,8 @@ def upsert_context_section(
             elif end_idx != -1:
                 # Corrupted: end marker without start — replace BOF through end marker
                 end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
                 if end_of_marker < len(content) and content[end_of_marker] == "\n":
                     end_of_marker += 1
                 new_content = section + content[end_of_marker:]
@@ -549,19 +554,32 @@ def remove_context_section(self, project_root: Path) -> bool:
             start_idx if start_idx != -1 else 0,
         )
 
-        if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
+        if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
+            removal_start = start_idx
+            removal_end = end_idx + len(self.CONTEXT_MARKER_END)
+        elif start_idx != -1:
+            # Corrupted: start marker without end — remove from start through EOF
+            removal_start = start_idx
+            removal_end = len(content)
+        elif end_idx != -1:
+            # Corrupted: end marker without start — remove BOF through end marker
+            removal_start = 0
+            removal_end = end_idx + len(self.CONTEXT_MARKER_END)
+        else:
             return False
 
-        end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
-        if end_of_marker < len(content) and content[end_of_marker] == "\n":
-            end_of_marker += 1
+        # Consume trailing line ending (CRLF or LF)
+        if removal_end < len(content) and content[removal_end] == "\r":
+            removal_end += 1
+        if removal_end < len(content) and content[removal_end] == "\n":
+            removal_end += 1
 
         # Also strip a blank line before the section if present
-        if start_idx > 0 and content[start_idx - 1] == "\n":
-            if start_idx > 1 and content[start_idx - 2] == "\n":
-                start_idx -= 1
+        if removal_start > 0 and content[removal_start - 1] == "\n":
+            if removal_start > 1 and content[removal_start - 2] == "\n":
+                removal_start -= 1
 
-        new_content = content[:start_idx] + content[end_of_marker:]
+        new_content = content[:removal_start] + content[removal_end:]
 
         # Normalize line endings before comparisons
         normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")

templates/commands/plan.md

@@ -148,5 +148,5 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 ## Key rules
 
-- Use absolute paths
+- Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
 - ERROR on gate failures or unresolved clarifications