Memory management:

* Add renaming with auto-updated references
  * More specific identifier naming (use term unmarked_memories)

Improve memory documentation:
  * Explain reference concept
  * Explain rationale

Add memory CLI commands
  * CRUD operations

CHANGELOG.md

@@ -10,6 +10,20 @@ Status of the `main` branch. Changes prior to the next official version change w
   - Modal markup cleanup: extract shared CSS classes (`.modal-info`, `.modal-hint`, `.modal-prompt`, `.modal-field`, `.modal-input`, `.modal-select`, `.modal-textarea`, `.modal-actions`, `.btn-secondary`) and remove duplicated inline styles from all seven modals. Inputs and textareas get an accent-colored focus ring; the modal backdrop has a subtle blur.
   - Add Language: replace the native `<select>` with a filterable combobox — type to filter, keyboard navigation (Up/Down/Enter/Esc), substring highlight, click-outside to close. The typed value is validated against the available languages list before submission.
 
+* Memories:
+  - Memories can now reference each other using the `` `mem:NAME` `` convention. Renames
+    propagate to all references automatically. See the [reference convention](https://oraios.github.io/serena/02-usage/045_memories.html#referencing-memories-from-other-memories).
+  - New `serena memories` CLI command group: `list`, `read`, `write`, `check` (referential
+    integrity report) and `auto-prefix-references` (heuristic rewrite of bare occurrences).
+    See the [CLI subcommands](https://oraios.github.io/serena/02-usage/045_memories.html#cli-subcommands).
+  - Onboarding now seeds a `memory_maintenance` memory describing the memory-style and
+    routing conventions, and the agent is instructed to read it before writing any other
+    memories. A `global/memory_maintenance` memory takes precedence over the per-project
+    seed. See the [memory maintenance section](https://oraios.github.io/serena/02-usage/045_memories.html#the-memory-maintenance-memory).
+  - Onboarding prompt rewritten to target a layout of `mem:core` (routing entry point),
+    `mem:suggested_commands`, `mem:tech_stack`, `mem:conventions`, `mem:task_completion`,
+    and optional per-module `mem:<module>/core` memories, using dense agent-notes style.
+
 * Tools:
   - `edit_memory`: New `dotall` parameter (default `False`) controlling whether ``.`` matches
     newlines in regex mode. **Behavior change**: previously DOTALL was forced on; the new default

docs/02-usage/040_workflow.md

@@ -143,9 +143,17 @@ and to store memories, which it can then draw upon in future interactions.
 
 In general, **memories** provide a way for Serena to store and retrieve 
 information about the project, relevant conventions, and other relevant aspects.
+Memories may reference each other using the `` `mem:NAME` `` convention; references
+are kept in sync across renames, and a `serena memories check` command is available
+to report stale references.
 
-For more information on this, including how to manage
-or disable these features, see [Memories & Onboarding](045_memories).
+During the first onboarding, Serena seeds a `memory_maintenance` memory describing the
+conventions (style, references, routing) that subsequent memories should follow, and the
+agent is instructed to read it before writing any project-specific memories.
+
+For more information on this, including the target memory layout, the `mem:` reference
+convention, the `serena memories` CLI subcommands, and how to manage or disable these
+features, see [Memories & Onboarding](045_memories).
 
 
 ## Preparing Your Project

docs/02-usage/045_memories.md

@@ -7,7 +7,7 @@ agent's internal memory management (e.g., `AGENTS.md` files).
 ## Memories
 
 Memories are simple, human-readable Markdown files that both you and
-your agent can create, read, and edit. 
+your agent can create, read, reference, and edit. 
 
 Serena differentiates between 
   * **project-specific memories**, which are stored in the `.serena/memories/` directory within your project folder, and
@@ -18,12 +18,76 @@ inferring appropriateness from the file name.
 When the agent starts working on a project, it receives the list of available memories. 
 The agent should be instructed to update memories by the user when appropriate.
 
+### Design Rationale
+
+Serena's memory system is intentionally minimal. It was designed to satisfy the following
+criteria:
+
+1. **Human-readable and editable.** Memories must remain directly readable and editable
+   in any text editor. The agent is typically the day-to-day consumer, but a human author
+   or reviewer must always be able to step in without going through the agent.
+2. **Versionable with the project.** Project memories live alongside the code and can
+   be committed, reviewed in PRs, and reverted like any other repository artifact.
+3. **Progressive disclosure.** Agents receive the full memory *name list* up
+   front as part of their initial instructions; any further routing is described inside
+   the memory content itself - typically a `mem:core` entry point pointing at focused
+   memories. The agent decides what to read based on names plus the routing it has
+   already seen.
+4. **Prefer routing to search.** Given an intelligent agent and well-structured routing, search is
+   unnecessary - and it adds noise: any retrieval method (lexical or semantic)
+   produces both false positives and false negatives. Explicit, name-based routing
+   decided by the agent is deterministic and avoids both error modes. Basic search via regex/grep
+   is sufficient to complement the routing when needed and is available to any agent.
+5. **Prefer deliberate reads to triggers.** The agent decides what to read and when. The harness does
+   not inject memory content on the agent's behalf.
+6. **Framework-agnostic.** The storage format is plain Markdown files in
+   a simple directory layout. The only Serena-specific convention is the `mem:` 
+   prefix for references to memories, which does not prevent using the memory files outside
+   of Serena.
+7. **Configurable and composable.** Two orthogonal memory scopes -
+   [per-project](#memories) (committed alongside the code) and [global](global-memories)
+   (shared across all your projects) - can be combined freely. Within either scope,
+   regex patterns in the global or project configuration can mark subsets as read-only
+   or [hide them entirely](#ignoring-memories) from the agent. This lets a project mix
+   personal cross-project knowledge with checked-in project conventions, and selectively
+   freeze either set, without custom plumbing.
+
+Taken together, these criteria rule out several common alternatives:
+
+- **Database-backed memory** (SQLite, graph databases, vector stores) is excluded by
+  criteria 1, 4, and 6.
+- **`AGENTS.md` and similar single-file conventions** are excluded by criteria 3 and 5.
+- **Hooks and harness-internal memory systems** are excluded by criteria 5 and 6.
+
+To our knowledge, no existing system satisfies our design goal, which is
+why Serena ships its own memory layer rather than reusing one.
+The closest existing approaches are in the family of Markdown-based personal knowledge
+management tools - **Obsidian**, **Logseq**, **Foam**.
+
 ### Organizing Memories
 
 Memories can be organized into **topics** by using `/` in the memory name (e.g. `modules/frontend`).
 The structure is mapped to the file system, where topics correspond to subdirectories.
 The `list_memories` tool can filter by topic, allowing the agent to explore even large numbers of memories in a structured way.
 
+(memory-references)=
+### Referencing Memories from Other Memories
+
+Memories may reference each other. Serena recognizes a reference as a memory name prefixed with
+`mem:` and wrapped in backticks, for example `` `mem:auth/login` `` or `` `mem:suggested_commands` ``.
+This convention has two practical consequences:
+
+- **Renames keep references intact.** When you rename or move a memory with the `rename_memory`
+  tool, Serena rewrites every `` `mem:OLD_NAME` `` occurrence across all memories to point to
+  the new name. References that do not use the `mem:` prefix will not be updated automatically.
+- **Integrity checks** (see [below](memory-cli)) report any `` `mem:NAME` `` whose target does
+  not resolve to an existing memory, and propose similarly-named candidates as likely intended
+  targets.
+
+The full convention - including style, add/update thresholds, and how to structure routing across
+`core` memories - is shipped to every onboarded project as the `memory_maintenance` memory; see the
+[Onboarding section](onboarding) below.
+
 (global-memories)=
 ### Global Memories
 
@@ -49,7 +113,7 @@ global or project-level [configuration](050_configuration):
 ignored_memory_patterns: ["_archive/.*", "_episodes/.*"]
 ```
 
-Ignored memories are completely excluded — they cannot be accessed via `read_memory`, `write_memory`,
+Ignored memories are completely excluded - they cannot be accessed via `read_memory`, `write_memory`,
 or any other memory tool. To read an ignored memory file, use the `read_file` tool on the raw file path
 (e.g., `.serena/memories/_archive/2026-03/some-topic.md`).
 
@@ -66,8 +130,8 @@ viewing, creating, editing, and deleting memories while Serena is running.
 
 By default, Serena performs an **onboarding process** when it encounters a project
 for the first time (i.e., when no project memories exist yet).
-The goal of the onboarding is for Serena to get familiar with the project —
-its structure, build system, testing setup, and other essential aspects —
+The goal of the onboarding is for Serena to get familiar with the project -
+its structure, build system, testing setup, and other essential aspects -
 and to store this knowledge as memories for future interactions.
 
 In further project activations, Serena will check whether onboarding was already
@@ -80,7 +144,32 @@ process if memories are found.
    performed (by checking if any memories exist).
 2. If no memories are found, Serena triggers the onboarding process, which
    reads key files and directories to understand the project.
-3. The gathered information is written into project-specific memory files (see above).
+3. Before any project memory is written, Serena materializes a project-local
+   `memory_maintenance` memory (see below). The agent is then instructed to read it
+   first and follow the conventions it describes.
+4. The gathered information is written into project-specific memory files following
+   the onboarding prompt instructions and the conventions outlined in `memory_maintenance`.
+
+(memory-maintenance-memory)=
+### The `memory_maintenance` Memory
+
+To make memory conventions discoverable to both the LLM and the user, Serena seeds
+a `memory_maintenance` memory on first onboarding. The seed is copied from a template
+shipped with the Serena package and contains the dense agent-notes style, the
+`mem:` reference convention, the routing model around `core` memories, the
+add/update threshold, and the maintenance actions (rename / delete / split).
+
+The seeding follows a strict precedence:
+
+1. If you already maintain a `global/memory_maintenance` memory, Serena uses that
+   and **does not** create a project-local copy. This is the recommended approach
+   for teams that want one shared convention document across all projects.
+2. Otherwise, if the project already has a `memory_maintenance` memory, it is left
+   untouched.
+3. Otherwise, the shipped template is written to `.serena/memories/memory_maintenance.md`.
+
+Existing files are never overwritten - you can freely customize the project copy.
+To refresh from the shipped template, delete the existing memory first.
 
 ### Tips for Onboarding
 
@@ -92,6 +181,29 @@ process if memories are found.
 - **Review the results**: After onboarding, we recommend having a quick look at the
   generated memories and editing them or adding new ones as needed.
 
+(memory-cli)=
+### CLI Subcommands
+
+While the recommended way to manage memories is through the **MCP integration**, 
+Serena also offers memory-related CLI commands.
+
+The following commands have **no MCP tool counterpart** and are intended for human execution:
+
+- `serena memories check` — referential-integrity report. By default reports only stale
+  `` `mem:NAME` `` references whose target does not resolve. Pass `--include-unmarked` to
+  also report bare occurrences of existing memory names found through a heuristic.
+- `serena memories auto-prefix-references` — heuristic rewrite of bare occurrences to add
+  the `mem:` prefix; supports `--dry-run`.
+- `serena memories initialize` will seed the `memory_maintenance` memory for the project.
+
+The remaining commands mirror the MCP tools, you can thus instruct your agent to manage memories with
+serena without having a running MCP server. Discover the full surface and per-command flags via:
+
+```shell
+serena memories --help
+serena memories <subcommand> --help
+```
+
 ## Disabling Memories and Onboarding
 
 If you do not require the functionality described in this section, you can selectively disable it.

src/serena/cli.py

@@ -9,7 +9,7 @@ import time
 from collections.abc import Iterator, Sequence
 from logging import Logger
 from pathlib import Path
-from typing import Any, Literal
+from typing import TYPE_CHECKING, Any, Literal
 
 import click
 from sensai.util import logging
@@ -43,6 +43,9 @@ from solidlsp.ls_config import Language
 from solidlsp.ls_types import SymbolKind
 from solidlsp.util.subprocess_util import subprocess_kwargs
 
+if TYPE_CHECKING:
+    from serena.project import MemoriesManager
+
 log = logging.getLogger(__name__)
 
 _MAX_CONTENT_WIDTH = 200
@@ -1124,14 +1127,43 @@ class MemoryCommands(AutoRegisteringGroup):
         )
 
     @staticmethod
-    def _load_memories_manager(project: str):
-        """Load the active project and return its memories manager."""
+    def _load_memories_manager(project: str) -> "MemoriesManager":
+        """
+        Load the project at ``project`` and return its memories manager.
+
+        Requires the project to already be a Serena project (``.serena/project.yml`` must
+        exist at the configured location). Never auto-creates the ``.serena`` directory —
+        if no project configuration is found, the user is directed at ``serena project create``.
+        """
         from serena.project import Project
 
         serena_config = SerenaConfig.from_config_file()
-        proj = Project.load(os.path.abspath(project), serena_config=serena_config)
+        project_path = os.path.abspath(project)
+        try:
+            proj = Project.load(project_path, serena_config=serena_config, autogenerate=False)
+        except FileNotFoundError as e:
+            raise click.UsageError(
+                f"{e}\nNo Serena project found at {project_path}. Create one first with:\n  serena project create {project_path}"
+            ) from e
         return proj.memories_manager
 
+    @staticmethod
+    @click.command(
+        "initialize",
+        help=(
+            "Initialize this project's memory layout by seeding the `memory_maintenance` memory. "
+            "Requires the project to already exist as a Serena project (run `serena project create` first); "
+            "this command does not create a `.serena` directory on its own. "
+            "If a `global/memory_maintenance` memory exists, it takes precedence and no project copy is created."
+        ),
+        context_settings={"max_content_width": _MAX_CONTENT_WIDTH},
+    )
+    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
+    def initialize(project: str) -> None:
+        manager = MemoryCommands._load_memories_manager(project)
+        name = manager.ensure_memory_maintenance_memory()
+        click.echo(f"Memory maintenance memory ready: `mem:{name}`.")
+
     @staticmethod
     @click.command(
         "list",
@@ -1184,20 +1216,114 @@ class MemoryCommands(AutoRegisteringGroup):
         manager = MemoryCommands._load_memories_manager(project)
         click.echo(manager.save_memory(memory_name, content, is_tool_context=False))
 
+    @staticmethod
+    @click.command(
+        "delete",
+        help="Delete a memory file. Use the `global/` prefix to address a global memory (e.g. `global/style_guide`).",
+        context_settings={"max_content_width": _MAX_CONTENT_WIDTH},
+    )
+    @click.argument("memory_name", type=str)
+    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
+    def delete(memory_name: str, project: str) -> None:
+        manager = MemoryCommands._load_memories_manager(project)
+        click.echo(manager.delete_memory(memory_name, is_tool_context=False))
+
+    @staticmethod
+    @click.command(
+        "rename",
+        help=(
+            "Rename or move a memory and update every `mem:OLD_NAME` reference across all memories. "
+            "Use `/` in the name to organize into topics; use the `global/` prefix to address a "
+            "global memory. Moving between project and global scope is supported."
+        ),
+        context_settings={"max_content_width": _MAX_CONTENT_WIDTH},
+    )
+    @click.argument("old_name", type=str)
+    @click.argument("new_name", type=str)
+    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
+    def rename(old_name: str, new_name: str, project: str) -> None:
+        manager = MemoryCommands._load_memories_manager(project)
+        message, n_refs = manager.rename_memory_and_propagate_references(old_name, new_name, is_tool_context=False)
+        click.echo(message)
+        if n_refs > 0:
+            click.echo(f"Updated {n_refs} `mem:` reference occurrence(s) across the memory graph.")
+
+    @staticmethod
+    @click.command(
+        "edit",
+        help=(
+            "Replace content matching a pattern in a memory. By default operates in literal "
+            "(non-regex) mode and refuses to replace more than one occurrence; pass --mode regex "
+            "to enable regex matching and --allow-multiple-occurrences to permit multiple hits."
+        ),
+        context_settings={"max_content_width": _MAX_CONTENT_WIDTH},
+    )
+    @click.argument("memory_name", type=str)
+    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
+    @click.option("--needle", type=str, required=True, help="The text to search for (literal by default; regex if --mode=regex).")
+    @click.option("--repl", type=str, required=True, help="The replacement text (verbatim).")
+    @click.option(
+        "--mode",
+        type=click.Choice(["literal", "regex"]),
+        default="literal",
+        show_default=True,
+        help="Treat --needle as literal text or as a Python regex (MULTILINE flag is always on; DOTALL via --dotall).",
+    )
+    @click.option(
+        "--allow-multiple-occurrences",
+        is_flag=True,
+        default=False,
+        help="Permit and apply multiple matches; without this, multiple matches raise an error.",
+    )
+    @click.option(
+        "--dotall",
+        is_flag=True,
+        default=False,
+        help="Regex mode only: make `.` match newlines as well, enabling multi-line patterns. Use with care.",
+    )
+    def edit(
+        memory_name: str,
+        project: str,
+        needle: str,
+        repl: str,
+        mode: Literal["literal", "regex"],
+        allow_multiple_occurrences: bool,
+        dotall: bool,
+    ) -> None:
+        manager = MemoryCommands._load_memories_manager(project)
+        click.echo(
+            manager.edit_memory(
+                memory_name,
+                needle,
+                repl,
+                mode,
+                allow_multiple_occurrences,
+                is_tool_context=False,
+                dotall=dotall,
+            )
+        )
+
     @staticmethod
     @click.command(
         "check",
         help=(
             "Check referential integrity across all memories of the project (and global memories). "
-            "Reports stale `mem:` references and unmarked-reference warnings split into high- and "
-            "low-confidence groups. Read-only and never writes. Always exits 0."
+            "Reports stale `mem:` references. With --include-unmarked, also reports bare occurrences "
+            "of existing memory names that lack the `mem:` prefix (split into high- and low-confidence). "
+            "Read-only and never writes. Always exits 0."
         ),
         context_settings={"max_content_width": _MAX_CONTENT_WIDTH},
     )
     @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
-    def check(project: str) -> None:
+    @click.option(
+        "--include-unmarked",
+        is_flag=True,
+        default=False,
+        help="Also report potentially unmarked references (bare occurrences of memory names without the `mem:` prefix).",
+    )
+    def check(project: str, include_unmarked: bool) -> None:
         manager = MemoryCommands._load_memories_manager(project)
-        report = manager.validate_referential_integrity()
+        report = manager.validate_referential_integrity(include_unmarked=include_unmarked)
         click.echo(report.format())
 
     @staticmethod

src/serena/project.py

@@ -166,6 +166,9 @@ class MemoriesManager:
     # generic prose word like "repository" is a substring of "serena_repository_structure"
     # but their token Jaccard is only 1/3, so we reject it at this floor.
     _FUZZY_BARE_TOKEN_JACCARD_FLOOR: float = 0.5
+
+    _WORDS_TO_IGNORE_AS_MEMORY_NAME_CANDIDATES: frozenset[str] = frozenset({"core"})
+    """Names that we specifically mention in our instructions and that coincide with common words"""
     _VERSION_SUFFIX_PATTERN = re.compile(r"_(?:v\d+|old|new|legacy|bak)$", re.IGNORECASE)
 
     @classmethod
@@ -507,19 +510,19 @@ class MemoriesManager:
         Outcome of :meth:`MemoriesManager.validate_referential_integrity`.
 
         :ivar stale_references: ``mem:NAME`` references whose target memory does not exist.
-        :ivar high_confidence_warnings: bare references whose suspected target name is unlikely
+        :ivar high_confidence_unmarked_memories: bare references whose suspected target name is unlikely
             to be coincidental prose (topic-path or sufficiently long).
-        :ivar low_confidence_warnings: bare references whose suspected target name could plausibly
+        :ivar low_confidence_unmarked_memories: bare references whose suspected target name could plausibly
             appear in ordinary prose (short, flat names).
         """
 
         stale_references: list["MemoriesManager.StaleReference"] = field(default_factory=list)
-        high_confidence_warnings: list["MemoriesManager.UnmarkedReferenceWarning"] = field(default_factory=list)
-        low_confidence_warnings: list["MemoriesManager.UnmarkedReferenceWarning"] = field(default_factory=list)
+        high_confidence_unmarked_memories: list["MemoriesManager.UnmarkedReferenceWarning"] = field(default_factory=list)
+        low_confidence_unmarked_memories: list["MemoriesManager.UnmarkedReferenceWarning"] = field(default_factory=list)
 
         def is_clean(self) -> bool:
             """:return: True iff no stale references and no warnings of any confidence level were found."""
-            return not (self.stale_references or self.high_confidence_warnings or self.low_confidence_warnings)
+            return not (self.stale_references or self.high_confidence_unmarked_memories or self.low_confidence_unmarked_memories)
 
         def format(self) -> str:
             """:return: a human-readable rendering suitable for CLI display."""
@@ -543,8 +546,8 @@ class MemoriesManager:
 
             # unmarked-reference warnings, split by confidence
             for label, warnings in (
-                ("High-confidence unmarked references", self.high_confidence_warnings),
-                ("Low-confidence unmarked references", self.low_confidence_warnings),
+                ("High-confidence unmarked references", self.high_confidence_unmarked_memories),
+                ("Low-confidence unmarked references", self.low_confidence_unmarked_memories),
             ):
                 if not warnings:
                     continue
@@ -714,6 +717,31 @@ class MemoriesManager:
 
         return f"Memory renamed from {old_name} to {new_name}."
 
+    def rename_memory_and_propagate_references(self, old_name: str, new_name: str, is_tool_context: bool) -> tuple[str, int]:
+        """
+        Renames a memory and updates every ``mem:OLD_NAME`` reference across all memories.
+
+        Memories whose content does not contain a reference to ``old_name`` are left
+        untouched (no spurious mtime changes). Memories that do are rewritten via
+        :meth:`save_memory`.
+
+        :param old_name: the current memory name (the source of the rename)
+        :param new_name: the target memory name
+        :param is_tool_context: forwarded to :meth:`save_memory` for read-only enforcement
+        :return: a tuple of (rename message returned by :meth:`move_memory`, total number of
+            ``mem:`` reference occurrences rewritten across all memories).
+        """
+        renaming_message = self.move_memory(old_name, new_name, is_tool_context=is_tool_context)
+
+        total_updates = 0
+        for memory_name in self.list_memories().get_full_list():
+            content = self.load_memory(memory_name)
+            updated_content, n_replacements = self.rename_references_to_memory(content, old_name, new_name)
+            if n_replacements > 0:
+                self.save_memory(memory_name, updated_content, is_tool_context=is_tool_context)
+                total_updates += n_replacements
+        return renaming_message, total_updates
+
     def edit_memory(
         self,
         name: str,
@@ -760,7 +788,7 @@ class MemoriesManager:
         source_basename = source_memory.rsplit("/", 1)[-1]
         return suspected_name == source_basename
 
-    def validate_referential_integrity(self) -> "MemoriesManager.ReferentialIntegrityReport":
+    def validate_referential_integrity(self, include_unmarked: bool = True) -> "MemoriesManager.ReferentialIntegrityReport":
         """
         Scans every (non-ignored) memory's content for referential integrity issues.
 
@@ -773,7 +801,8 @@ class MemoriesManager:
         * **exact unmarked-reference warnings** — bare occurrences of an existing memory
           name that appear without the ``mem:`` prefix. Split into high-confidence (the
           suspected name contains a ``/`` or exceeds :attr:`_HIGH_CONFIDENCE_NAME_LENGTH`)
-          and low-confidence groups.
+          and low-confidence groups. Candidate names whose basename matches
+          :attr:`WORDS_TO_IGNORE_AS_MEMORY_NAME_CANDIDATES` are skipped.
         * **fuzzy near-miss warnings** — long, distinctive bare tokens in a memory body
           that *do not* match an existing name exactly but similarity-match a
           high-confidence existing name AND share at least :attr:`_FUZZY_BARE_TOKEN_JACCARD_FLOOR`
@@ -787,6 +816,8 @@ class MemoriesManager:
 
         This method has no side effects.
 
+        :param include_unmarked: if False, skip the two unmarked-reference scans (exact and
+            fuzzy near-miss) entirely; only stale references are reported.
         :return: a :class:`ReferentialIntegrityReport` summarizing all findings.
         """
         report = MemoriesManager.ReferentialIntegrityReport()
@@ -801,6 +832,10 @@ class MemoriesManager:
         high_confidence_names = [n for n in all_names if "/" in n or len(n) >= self._HIGH_CONFIDENCE_NAME_LENGTH]
 
         for source_name in all_names:
+            # content of this memory should not be analyzed regarding stale references
+            if source_name == self.MEMORY_MAINTENANCE_NAME:
+                continue
+
             content = self.load_memory(source_name)
             if not content:
                 # skip empty memories silently — no references can exist in empty content
@@ -823,10 +858,16 @@ class MemoriesManager:
                     )
                 )
 
+            if not include_unmarked:
+                continue
+
             # exact unmarked references: bare occurrences of any existing memory name (except self)
             for candidate_name in all_names:
                 if self._is_self_reference(source_name, candidate_name):
                     continue
+                # skip candidate names whose basename is an ambiguous common word
+                if candidate_name.rsplit("/", 1)[-1] in self._WORDS_TO_IGNORE_AS_MEMORY_NAME_CANDIDATES:
+                    continue
                 n = self._find_bare_occurrences(content, candidate_name)
                 if n == 0:
                     continue
@@ -840,9 +881,9 @@ class MemoriesManager:
                     actual_token=candidate_name,
                 )
                 if is_high_conf:
-                    report.high_confidence_warnings.append(warning)
+                    report.high_confidence_unmarked_memories.append(warning)
                 else:
-                    report.low_confidence_warnings.append(warning)
+                    report.low_confidence_unmarked_memories.append(warning)
 
             # fuzzy near-misses: long bare tokens that similarity-match a high-confidence existing name
             for token, n in self._iter_long_bare_tokens(content):
@@ -855,6 +896,8 @@ class MemoriesManager:
                 for existing in high_confidence_names:
                     if self._is_self_reference(source_name, existing):
                         continue
+                    if existing.rsplit("/", 1)[-1] in self._WORDS_TO_IGNORE_AS_MEMORY_NAME_CANDIDATES:
+                        continue
                     score = self.compute_name_similarity(token, existing)
                     if score < self.NAME_SIMILARITY_THRESHOLD:
                         continue
@@ -873,7 +916,7 @@ class MemoriesManager:
                         best_name = existing
                 if best_name is None:
                     continue
-                report.high_confidence_warnings.append(
+                report.high_confidence_unmarked_memories.append(
                     MemoriesManager.UnmarkedReferenceWarning(
                         source_memory=source_name,
                         suspected_name=best_name,
@@ -933,11 +976,11 @@ class MemoriesManager:
         validation = self.validate_referential_integrity()
 
         # combine the warning groups according to the include_flat_names policy
-        warnings: list[MemoriesManager.UnmarkedReferenceWarning] = list(validation.high_confidence_warnings)
+        warnings: list[MemoriesManager.UnmarkedReferenceWarning] = list(validation.high_confidence_unmarked_memories)
         if include_flat_names:
-            warnings.extend(validation.low_confidence_warnings)
+            warnings.extend(validation.low_confidence_unmarked_memories)
         else:
-            report.skipped_flat.extend(validation.low_confidence_warnings)
+            report.skipped_flat.extend(validation.low_confidence_unmarked_memories)
 
         # apply replacements per source memory, grouping warnings to avoid re-reading content
         warnings_by_source: dict[str, list[MemoriesManager.UnmarkedReferenceWarning]] = {}

src/serena/tools/memory_tools.py

@@ -82,13 +82,11 @@ class RenameMemoryTool(Tool, ToolMarkerCanEdit):
         The "global" topic should only be used if explicitly instructed.
         References to other memories that are marked with the `mem:` prefix will be updated accordingly.
         """
-        renaming_message = self.memories_manager.move_memory(old_name, new_name, is_tool_context=True)
-        for memory in self.memories_manager.list_memories().get_full_list():
-            memory_content = self.memories_manager.load_memory(memory)
-            updated_content, n_replacements = self.memories_manager.rename_references_to_memory(memory_content, old_name, new_name)
-            if n_replacements > 0:
-                log.info(f"Updated {n_replacements} references to memory {old_name} to {new_name}")
-                self.memories_manager.save_memory(memory, updated_content, is_tool_context=True)
+        renaming_message, n_references_updated = self.memories_manager.rename_memory_and_propagate_references(
+            old_name, new_name, is_tool_context=True
+        )
+        if n_references_updated > 0:
+            log.info(f"Updated {n_references_updated} references to memory {old_name} to {new_name}")
         return renaming_message
 
 

test/serena/test_memories_manager.py

@@ -278,21 +278,21 @@ class TestValidateReferentialIntegrity:
         _write(fs_manager, "auth/login", "# notes")
         _write(fs_manager, "docs", "the auth/login process is documented elsewhere")
         report = fs_manager.validate_referential_integrity()
-        assert len(report.high_confidence_warnings) == 1
-        warning = report.high_confidence_warnings[0]
+        assert len(report.high_confidence_unmarked_memories) == 1
+        warning = report.high_confidence_unmarked_memories[0]
         assert warning.suspected_name == "auth/login"
         assert warning.is_high_confidence is True
         assert warning.occurrences == 1
-        assert report.low_confidence_warnings == []
+        assert report.low_confidence_unmarked_memories == []
 
     def test_low_confidence_unmarked_warning_for_short_flat_name(self, fs_manager: MemoriesManager) -> None:
         _write(fs_manager, "auth", "# notes")
         _write(fs_manager, "docs", "you must use auth here")
         report = fs_manager.validate_referential_integrity()
-        assert report.high_confidence_warnings == []
-        assert len(report.low_confidence_warnings) == 1
-        assert report.low_confidence_warnings[0].suspected_name == "auth"
-        assert report.low_confidence_warnings[0].is_high_confidence is False
+        assert report.high_confidence_unmarked_memories == []
+        assert len(report.low_confidence_unmarked_memories) == 1
+        assert report.low_confidence_unmarked_memories[0].suspected_name == "auth"
+        assert report.low_confidence_unmarked_memories[0].is_high_confidence is False
 
     def test_long_flat_name_is_high_confidence(self, fs_manager: MemoriesManager) -> None:
         # a flat name >= _HIGH_CONFIDENCE_NAME_LENGTH chars is unlikely to be coincidental prose
@@ -301,7 +301,7 @@ class TestValidateReferentialIntegrity:
         _write(fs_manager, long_name, "# notes")
         _write(fs_manager, "docs", f"the {long_name} is documented here")
         report = fs_manager.validate_referential_integrity()
-        assert len(report.high_confidence_warnings) == 1
+        assert len(report.high_confidence_unmarked_memories) == 1
 
     def test_fuzzy_near_miss_rejects_substring_only_matches(self, fs_manager: MemoriesManager) -> None:
         """
@@ -328,8 +328,8 @@ class TestValidateReferentialIntegrity:
         )
         report = fs_manager.validate_referential_integrity()
         assert report.is_clean(), (
-            f"Expected no findings; got high={report.high_confidence_warnings}, "
-            f"low={report.low_confidence_warnings}, stale={report.stale_references}"
+            f"Expected no findings; got high={report.high_confidence_unmarked_memories}, "
+            f"low={report.low_confidence_unmarked_memories}, stale={report.stale_references}"
         )
 
     def test_long_flat_name_near_miss_is_high_confidence(self, fs_manager: MemoriesManager) -> None:
@@ -350,12 +350,12 @@ class TestValidateReferentialIntegrity:
         _write(fs_manager, "docs", f"See {bare} for details")
 
         report = fs_manager.validate_referential_integrity()
-        assert len(report.high_confidence_warnings) == 1, (
+        assert len(report.high_confidence_unmarked_memories) == 1, (
             f"expected one high-confidence warning for the near-miss reference, "
-            f"got {len(report.high_confidence_warnings)} "
-            f"(high={report.high_confidence_warnings}, low={report.low_confidence_warnings})"
+            f"got {len(report.high_confidence_unmarked_memories)} "
+            f"(high={report.high_confidence_unmarked_memories}, low={report.low_confidence_unmarked_memories})"
         )
-        warning = report.high_confidence_warnings[0]
+        warning = report.high_confidence_unmarked_memories[0]
         assert warning.suspected_name == existing
         assert warning.source_memory == "docs"
 
@@ -367,7 +367,7 @@ class TestValidateReferentialIntegrity:
         # `auth/login` mentioning its own basename `login` should not produce a warning;
         # `auth` mentioned in `auth/login` content also shouldn't (it's the prefix), and only
         # actual matches matter — assert no warning concerns the source itself
-        for w in report.high_confidence_warnings + report.low_confidence_warnings:
+        for w in report.high_confidence_unmarked_memories + report.low_confidence_unmarked_memories:
             assert not (w.source_memory == "auth/login" and w.suspected_name in ("login", "auth/login"))
 
     def test_marked_reference_does_not_produce_unmarked_warning(self, fs_manager: MemoriesManager) -> None:
@@ -382,8 +382,8 @@ class TestValidateReferentialIntegrity:
         _write(fs_manager, "docs", "we have `mem:auth/login` plus a bare auth/login mention")
         report = fs_manager.validate_referential_integrity()
         # only the bare occurrence should be counted
-        assert len(report.high_confidence_warnings) == 1
-        assert report.high_confidence_warnings[0].occurrences == 1
+        assert len(report.high_confidence_unmarked_memories) == 1
+        assert report.high_confidence_unmarked_memories[0].occurrences == 1
 
     def test_empty_memory_skipped(self, fs_manager: MemoriesManager) -> None:
         _write(fs_manager, "auth/login", "")
@@ -397,7 +397,7 @@ class TestValidateReferentialIntegrity:
         _write(manager, "frozen/notes", "see bare auth/login mention")
         _write(manager, "auth/login", "# notes")
         report = manager.validate_referential_integrity()
-        warnings = report.high_confidence_warnings
+        warnings = report.high_confidence_unmarked_memories
         assert len(warnings) == 1
         assert warnings[0].source_memory == "frozen/notes"
         assert warnings[0].source_is_read_only is True