refactor: rename atomic flags for clarity and remove atomic-apply

- Rename --atomic to --atomic-identifiers for clarity
- Rename --no-atomic to --no-atomic-identifiers
- Remove --atomic-apply flag (always atomic by default)
- Keep --atomic-search and --atomic-replace unchanged
- Update all CLI handlers, docs, MCP server, and tests
- All tests passing (536 tests in Rust, 63 in MCP, VS Code clean)

This prevents confusion between identifier atomicity (treating compound
words as single units) and transactional apply operations.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: ndbroadbent

docs/src/content/docs/commands/apply.mdx

@@ -19,7 +19,6 @@ renamify apply [ID] [OPTIONS]
 
 ## Options
 
-- `--atomic` - Apply changes atomically (default: true)
 - `--commit` - Create a git commit after applying
 - `--force-with-conflicts` - Apply even if conflicts are detected
 

docs/src/content/docs/commands/plan.mdx

@@ -66,10 +66,10 @@ Note: The plan is always saved to `.renamify/plan.json` (or the path specified b
 "Atomic" means treating a search or replace identifier as a single unit,
 not splitting it into separate components. E.g. GitHub → github, not git_hub
 
-- `--atomic` - Treat both search and replace terms as indivisible units
+- `--atomic-identifiers` - Treat both search and replace terms as indivisible units
 - `--atomic-search` - Only treat search term as atomic
 - `--atomic-replace` - Only treat replace term as atomic
-- `--no-atomic` - Disable atomic mode (override config)
+- `--no-atomic-identifiers` - Disable atomic mode (override config)
 - `--no-atomic-search` - Disable atomic for search term
 - `--no-atomic-replace` - Disable atomic for replace term
 
@@ -190,7 +190,7 @@ renamify plan old_name new_name --dry-run
 
 ```bash
 # Treat compound words as single units
-renamify plan DocSpring FormAPI --atomic
+renamify plan DocSpring FormAPI --atomic-identifiers
 
 # Only search term is atomic
 renamify plan DocSpring form_api --atomic-search

docs/src/content/docs/commands/rename.mdx

@@ -72,10 +72,10 @@ renamify rename <OLD> <NEW> [PATHS]... [OPTIONS]
 "Atomic" means treating a search or replace identifier as a single unit,
 not splitting it into separate components. E.g. GitHub → github, not git_hub
 
-- `--atomic` - Treat both search and replace terms as indivisible units
+- `--atomic-identifiers` - Treat both search and replace terms as indivisible units
 - `--atomic-search` - Only treat search term as atomic
 - `--atomic-replace` - Only treat replace term as atomic
-- `--no-atomic` - Disable atomic mode (override config)
+- `--no-atomic-identifiers` - Disable atomic mode (override config)
 - `--no-atomic-search` - Disable atomic for search term
 - `--no-atomic-replace` - Disable atomic for replace term
 
@@ -130,10 +130,10 @@ renamify rename oldApi newApi \
 
 ```bash
 # Treat compound words as single units
-renamify rename DocSpring FormAPI --atomic
+renamify rename DocSpring FormAPI --atomic-identifiers
 
-# Without --atomic, DocSpring would match doc_spring in snake_case
-# With --atomic, DocSpring only matches docspring (as single unit)
+# Without --atomic-identifiers, DocSpring would match doc_spring in snake_case
+# With --atomic-identifiers, DocSpring only matches docspring (as single unit)
 ```
 
 ### Case Style Control

docs/src/content/docs/commands/search.mdx

@@ -56,10 +56,10 @@ Available styles: `snake`, `kebab`, `camel`, `pascal`, `screaming-snake`,
 
 ### Atomic Mode
 
-- `--atomic` - Treat the search term as an indivisible unit (no word boundaries)
-- `--atomic-search` - Same as `--atomic` for search command
-- `--no-atomic` - Disable atomic mode (override config)
-- `--no-atomic-search` - Same as `--no-atomic` for search command
+- `--atomic-identifiers` - Treat the search term as an indivisible unit (no word boundaries)
+- `--atomic-search` - Same as `--atomic-identifiers` for search command
+- `--no-atomic-identifiers` - Disable atomic mode (override config)
+- `--no-atomic-search` - Same as `--no-atomic-identifiers` for search command
 
 ### Output Control
 
@@ -145,7 +145,7 @@ Search for compound words as single units:
 
 ```bash
 # DocSpring will match as a whole word, not doc_spring
-renamify search DocSpring --atomic
+renamify search DocSpring --atomic-identifiers
 ```
 
 ### JSON Output for Processing

docs/src/content/docs/features/atomic-identifiers.mdx

@@ -46,19 +46,22 @@ You can specify atomic mode using CLI flags:
 
 <Tabs>
 <TabItem label="Both atomic">
-  ```bash # Both search and replace terms are atomic renamify rename FormAPI
-  DocSpring --atomic
+  ```bash
+  # Both search and replace terms are atomic
+  renamify rename FormAPI DocSpring --atomic-identifiers
   ```
 </TabItem>
 <TabItem label="Search only">
-  ```bash # Only search term is atomic renamify rename FormAPI Helper
-  --atomic-search
+  ```bash
+  # Only search term is atomic
+  renamify rename FormAPI Helper --atomic-search
   ```
 </TabItem>
 <TabItem label="Replace only">
 
-```bash # Only replace term is atomic renamify rename OldName DocSpring
---atomic-replace
+```bash
+# Only replace term is atomic
+renamify rename OldName DocSpring --atomic-replace
 ```
 
 </TabItem>
@@ -97,7 +100,7 @@ renamify rename OldName DocSpring --no-atomic-replace
 When renaming "FormAPI" to "DocSpring" with atomic mode:
 
 ```bash
-renamify rename FormAPI DocSpring --atomic
+renamify rename FormAPI DocSpring --atomic-identifiers
 ```
 
 Results:

renamify-cli/src/cli/args.rs

@@ -124,21 +124,21 @@ pub struct AcronymArgs {
 /// Atomic identifier arguments
 #[derive(Args, Debug, Clone)]
 pub struct AtomicArgs {
-    /// Treat both terms as atomic (single words). E.g. DocSpring becomes docspring in snake_case, not doc_spring
+    /// Treat both search and replace terms as atomic identifiers (no word boundaries). E.g. GitHub becomes github in snake_case, not git_hub
     #[arg(long, conflicts_with_all = ["atomic_search", "atomic_replace"])]
-    pub atomic: bool,
+    pub atomic_identifiers: bool,
 
-    /// Treat search term as atomic (GitHub → github, not git_hub)
+    /// Treat search term as atomic identifier (GitHub → github, not git_hub)
     #[arg(long)]
     pub atomic_search: bool,
 
-    /// Treat replace term as atomic (GitHub → github, not git_hub)
+    /// Treat replace term as atomic identifier (GitHub → github, not git_hub)
     #[arg(long)]
     pub atomic_replace: bool,
 
-    /// Override config: allow word boundary detection
-    #[arg(long, conflicts_with = "atomic")]
-    pub no_atomic: bool,
+    /// Override config: allow word boundary detection for both terms
+    #[arg(long, conflicts_with = "atomic_identifiers")]
+    pub no_atomic_identifiers: bool,
 
     /// Override config for search: allow word boundaries
     #[arg(long, conflicts_with = "atomic_search")]
@@ -422,10 +422,6 @@ pub enum Commands {
         /// Plan ID or path to apply (optional - defaults to .renamify/plan.json)
         id: Option<String>,
 
-        /// Apply changes atomically
-        #[arg(long, default_value_t = true)]
-        atomic: bool,
-
         /// Commit changes to git
         #[arg(long)]
         commit: bool,

renamify-cli/src/main.rs

@@ -195,10 +195,10 @@ fn main() {
                 acronyms.exclude_acronyms,
                 acronyms.only_acronyms,
                 cli::args::AtomicArgs {
-                    atomic: false,
+                    atomic_identifiers: false,
                     atomic_search: false,
                     atomic_replace: false,
-                    no_atomic: false,
+                    no_atomic_identifiers: false,
                     no_atomic_search: false,
                     no_atomic_replace: false,
                 },
@@ -210,7 +210,6 @@ fn main() {
 
         Commands::Apply {
             id,
-            atomic: _,
             commit,
             force_with_conflicts,
             output,
@@ -258,7 +257,7 @@ fn main() {
             no_rename_root,
             dry_run,
             acronyms,
-            atomic: _, // Not implemented in rename yet
+            atomic,
             output,
             quiet,
         } => {
@@ -291,6 +290,7 @@ fn main() {
                 acronyms.include_acronyms,
                 acronyms.exclude_acronyms,
                 acronyms.only_acronyms,
+                atomic,
                 cli.yes,
                 use_color,
                 output,

renamify-cli/src/plan.rs

@@ -58,9 +58,9 @@ pub fn handle_plan(
 
     // Build atomic config from CLI args and config file
     let atomic_config = renamify_core::atomic::AtomicConfig::from_flags_and_config(
-        atomic.atomic,
-        atomic.atomic_search || (atomic.atomic && !atomic.no_atomic_search),
-        atomic.atomic_replace || (atomic.atomic && !atomic.no_atomic_replace),
+        atomic.atomic_identifiers,
+        atomic.atomic_search || (atomic.atomic_identifiers && !atomic.no_atomic_search),
+        atomic.atomic_replace || (atomic.atomic_identifiers && !atomic.no_atomic_replace),
         config.atomic,
     );
 

renamify-cli/src/rename.rs

@@ -2,7 +2,7 @@ use anyhow::Result;
 use renamify_core::{rename_operation, OutputFormatter, Style};
 use std::path::PathBuf;
 
-use crate::cli::{types::StyleArg, OutputFormat, PreviewArg};
+use crate::cli::{args::AtomicArgs, types::StyleArg, OutputFormat, PreviewArg};
 
 #[allow(clippy::too_many_arguments)]
 pub fn handle_rename(
@@ -31,6 +31,7 @@ pub fn handle_rename(
     include_acronyms: Vec<String>,
     exclude_acronyms: Vec<String>,
     only_acronyms: Vec<String>,
+    atomic: AtomicArgs,
     auto_approve: bool,
     use_color: bool,
     output: OutputFormat,
@@ -41,6 +42,17 @@ pub fn handle_rename(
     let include_styles: Vec<Style> = include_styles.into_iter().map(Into::into).collect();
     let only_styles: Vec<Style> = only_styles.into_iter().map(Into::into).collect();
 
+    // Load config to get atomic identifiers
+    let config = renamify_core::Config::load().unwrap_or_default();
+
+    // Build atomic config from CLI args and config file
+    let atomic_config = renamify_core::atomic::AtomicConfig::from_flags_and_config(
+        atomic.atomic_identifiers,
+        atomic.atomic_search || (atomic.atomic_identifiers && !atomic.no_atomic_search),
+        atomic.atomic_replace || (atomic.atomic_identifiers && !atomic.no_atomic_replace),
+        config.atomic,
+    );
+
     // Handle quiet mode - overrides preview to none unless output is json
     let effective_preview = if quiet && output != OutputFormat::Json {
         None
@@ -87,6 +99,7 @@ pub fn handle_rename(
         &include_acronyms,
         &exclude_acronyms,
         &only_acronyms,
+        Some(&atomic_config),
         auto_approve,
         use_color,
     )?;

renamify-cli/tests/train_case_e2e_test.rs

@@ -248,6 +248,7 @@ The Rename-Tool-Based-Solution is working.
         &[],    // include_acronyms
         &[],    // exclude_acronyms
         &[],    // only_acronyms
+        None,   // atomic_config
         true,   // auto_approve
         true,   // use_color
     )