fix: make config sync directories configurable via config.yaml

[LLQWQ]

Problem

CLI's FileSync and SettingSync have inconsistent handling of dot-prefixed directories like .agents:

• FileSync._collect_local_files() skips ALL dot-prefixed directories
• SettingSync uses _is_config_path() which treats ALL dot-prefixed dirs as config
• But SyncEngine._is_config() also treats ALL dot-prefixed dirs as config

This causes problems when syncing custom config directories:

1. If .agents/ exists on Obsidian but not on CLI vault, CLI won't send it to server
2. Server may then tell other devices to delete .agents/ files
3. Custom config directories get lost across devices

Impact

• Custom config directories (.agents, .my-config, etc.) are not properly synchronized
• Data loss when using CLI alongside Obsidian plugin
• Inconsistent behavior between FileSync and SettingSync

Root Cause

In file_sync.py:

first = rel.split("/")[0]
if first.startswith("."):
    continue  # Skips .agents/ files

In sync_engine.py:

def _is_config(self, rel_path: str) -> bool:
    first = rel_path.split("/")[0]
    return first.startswith(".")  # Too broad

Proposed Fix

Make config directory handling explicit:

1. Always treat .obsidian and .agents as config directories
2. Let other dot-prefixed dirs follow sync_config setting
3. FileSync should skip dot-prefixed dirs only when sync_config=True
   (so they go through SettingSync)

Files Changed

• fns_cli/config.py: Add config_sync_dirs to config schema
• fns_cli/file_sync.py: Skip dot-prefixed dirs based on config_sync_dirs
• fns_cli/setting_sync.py: Use config_sync_dirs for config path check
• fns_cli/sync_engine.py: Use explicit config directory list

Testing

1. Set up Obsidian plugin with .agents in configSyncOtherDirs
2. Add files to .agents/ directory in Obsidian
3. Run CLI sync on another device (without .agents/ directory)
4. Verify .agents/ files are synced to CLI
5. Run Obsidian sync again — .agents/ files should remain

Environment

• CLI version: latest (feat/setting-sync branch)
• OS: Linux/Any

Summary by Sourcery

Make config directories explicitly configurable and adjust sync behavior so dot-prefixed folders are treated as config only when configured, aligning FileSync, SettingSync, FolderSync, and SyncEngine.

New Features:

• Add configurable config_sync_dirs option in config.yaml to control which dot-prefixed directories are treated as config.

Enhancements:

• Align FileSync, SettingSync, FolderSync, and SyncEngine logic to consistently skip or handle dot-prefixed config directories based on config_sync_dirs and sync_config settings.
• Update initial sync and full file push logic to avoid uploading config directories through FileSync, delegating them to SettingSync instead.

[sourcery-ai]

Reviewer's Guide

Makes handling of dot-prefixed config directories explicit and configurable so that only selected directories (e.g. .obsidian, .agents) are treated as config and are synced via SettingSync, while FolderSync/FileSync ignore them appropriately based on sync_config/sync_files and config_sync_dirs in config.yaml.

Sequence diagram for deciding config vs file sync for dot-prefixed directories

sequenceDiagram
    actor User
    participant SyncEngine
    participant FileSync
    participant SettingSync
    participant FolderSync

    Note over User: User triggers a sync operation

    User->>SyncEngine: start_sync()
    SyncEngine->>SyncEngine: _initial_sync()

    Note over SyncEngine: Config: sync_files, sync_config, config_sync_dirs

    SyncEngine->>NoteSync: request_sync()
    NoteSync-->>SyncEngine: notes_synced

    alt sync_files is true
        SyncEngine->>FileSync: request_sync()
        FileSync-->>SyncEngine: file_sync_started
    end

    alt sync_config is true
        SyncEngine->>SettingSync: request_sync()
        SettingSync-->>SyncEngine: setting_sync_started
    end

    loop For each local file
        SyncEngine->>SyncEngine: _is_config(rel_path)
        Note over SyncEngine: first = rel_path.split("/")[0]
        alt first not dot-prefixed
            SyncEngine-->>SyncEngine: returns False
            alt sync_files is true
                SyncEngine->>FileSync: push_upload(rel_path)
            else sync_files is false
                SyncEngine-->>SyncEngine: skip file
            end
        else first dot-prefixed
            alt first in config_sync_dirs
                SyncEngine-->>SyncEngine: returns True
                alt sync_config is true
                    SyncEngine->>SettingSync: push_upload(rel_path)
                else sync_config is false
                    SyncEngine-->>SyncEngine: skip file
                end
            else first not in config_sync_dirs
                alt sync_config is true
                    SyncEngine-->>SyncEngine: returns True
                    SyncEngine->>SettingSync: push_upload(rel_path)
                else sync_config is false
                    SyncEngine-->>SyncEngine: returns False
                    alt sync_files is true
                        SyncEngine->>FileSync: push_upload(rel_path)
                    else sync_files is false
                        SyncEngine-->>SyncEngine: skip file
                    end
                end
            end
        end
    end

    Note over FolderSync: Handles folder events from server

    Server->>FolderSync: _on_sync_modify(msg)
    FolderSync->>FolderSync: first = rel_path.split("/")[0]
    alt first startswith dot
        FolderSync-->>FolderSync: log ignore and return
    else not dot-prefixed
        FolderSync->>FolderSync: mkdir for folder
    end

    Server->>FolderSync: _on_sync_delete(msg)
    FolderSync->>FolderSync: first = rel_path.split("/")[0]
    alt first startswith dot
        FolderSync-->>FolderSync: log ignore and return
    else not dot-prefixed
        FolderSync->>FolderSync: delete folder if exists
    end

    Server->>FolderSync: _on_sync_rename(msg)
    FolderSync->>FolderSync: check first segments of old and new
    alt either startswith dot
        FolderSync-->>FolderSync: log ignore and return
    else neither dot-prefixed
        FolderSync->>FolderSync: rename folder
    end

Loading

Class diagram for configurable config_sync_dirs and sync routing

classDiagram
    class SyncConfig {
        +list~str~ exclude_patterns
        +int file_chunk_size
        +list~str~ config_sync_dirs
    }

    class AppConfig {
        +SyncConfig sync
        +ClientConfig client
        +ServerConfig server
    }

    class SyncEngine {
        +AppConfig config
        +Path vault_path
        +FileSync file_sync
        +SettingSync setting_sync
        +NoteSync note_sync
        +FolderSync folder_sync
        +bool _is_note(rel_path)
        +bool _is_config(rel_path)
        +bool _should_sync_file(rel_path)
        +async _initial_sync()
        +async _push_all_files()
    }

    class FileSync {
        +AppConfig config
        +SyncEngine engine
        +list~dict~ _collect_local_files()
    }

    class SettingSync {
        +AppConfig config
        +SyncEngine engine
        +async request_sync()
        +async push_upload(rel_path)
    }

    class SettingSyncHelpers {
        +bool _is_config_path(rel, config_sync_dirs)
        +dict _extract_inner(msg_data)
    }

    class FolderSync {
        +Path vault_path
        +SyncEngine engine
        +async _on_sync_modify(msg)
        +async _on_sync_delete(msg)
        +async _on_sync_rename(msg)
    }

    class WSMessage {
        +dict data
    }

    class ConfigLoader {
        +AppConfig load_config(path)
    }

    SyncEngine --> SyncConfig : uses
    SyncEngine --> FileSync : coordinates
    SyncEngine --> SettingSync : coordinates
    SyncEngine --> FolderSync : coordinates

    AppConfig --> SyncConfig : has

    FileSync --> SyncEngine : engine

    SettingSync --> SyncEngine : engine

    FolderSync --> SyncEngine : engine

    ConfigLoader --> AppConfig : constructs

    SettingSyncHelpers --> SettingSync : utility
    SettingSyncHelpers ..> SyncConfig : uses config_sync_dirs

    SyncEngine ..> SyncConfig : uses config_sync_dirs
    FileSync ..> SyncConfig : uses config_sync_dirs and sync_config
    FolderSync ..> SyncConfig : indirectly uses via engine

Loading

File-Level Changes

Change	Details	Files
Introduce configurable list of config sync directories and wire it into sync logic	Add SyncConfig.config_sync_dirs with default ['.obsidian', '.agents'] Load config_sync_dirs from config.yaml into AppConfig Use config_sync_dirs when determining whether a path is treated as config in SyncEngine and SettingSync	fns_cli/config.py fns_cli/sync_engine.py fns_cli/setting_sync.py
Align FileSync, FolderSync, and SyncEngine behavior for dot-prefixed directories	FileSync now skips dot-prefixed directories only when sync_config is enabled, treating them as config handled by SettingSync SyncEngine._is_config now checks first path segment against config_sync_dirs and falls back to sync_config for other dot-dirs SyncEngine initial sync and _push_all_files logic updated so file sync runs based on sync_files and never uploads config files FolderSync now ignores create/delete/rename events for dot-prefixed directories, logging them as config dirs handled elsewhere	fns_cli/file_sync.py fns_cli/sync_engine.py fns_cli/folder_sync.py
Update SettingSync to use configurable config directories while remaining backward compatible	_is_config_path now accepts a config_sync_dirs parameter and checks first segment against it If a path is dot-prefixed but not listed, it is still treated as config by default to preserve prior behavior	fns_cli/setting_sync.py

Possibly linked issues

• #(unknown): They describe the same dot-prefixed config directory sync bug; the PR implements the issue’s proposed configuration-based fix.

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[sourcery-ai]

Hey - I've left some high level feedback:

• FolderSync currently hardcodes all dot-prefixed directories as config (skipping them unconditionally), which diverges from the new config_sync_dirs + sync_config logic used elsewhere; consider reusing the same _is_config/config logic here so FolderSync behavior stays consistent with FileSync/SettingSync.
• The new config_sync_dirs setting is only partially wired through (e.g., _is_config uses it but _is_config_path’s default behavior remains "all dot dirs are config" unless it is explicitly passed); it would be cleaner to ensure all config-path checks consistently receive and honor config_sync_dirs so the effective rules don’t differ between components.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- FolderSync currently hardcodes all dot-prefixed directories as config (skipping them unconditionally), which diverges from the new `config_sync_dirs` + `sync_config` logic used elsewhere; consider reusing the same `_is_config`/config logic here so FolderSync behavior stays consistent with FileSync/SettingSync.
- The new `config_sync_dirs` setting is only partially wired through (e.g., `_is_config` uses it but `_is_config_path`’s default behavior remains "all dot dirs are config" unless it is explicitly passed); it would be cleaner to ensure all config-path checks consistently receive and honor `config_sync_dirs` so the effective rules don’t differ between components.

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