fix: address code review findings on the bundle lifecycle

The user-origin marker on replaced mcp.json entries is now sticky:
re-records and cross-bundle transfers only upgrade replaced to
transferred when the prior record proves bundle origin, so updating a
bundle can no longer make uninstall delete a key the user had before the
bundle replaced it. Canonical source URLs lowercase only the host, since
self-hosted forges treat repository paths as case-sensitive and
collapsing distinct repos misdirects updates and uninstalls. git clone
invocations pass '--' before the URL so a crafted source cannot be
parsed as a git flag. Lifecycle flags (--install, --install-builtins,
--update-bundle, --uninstall) and their companions now conflict
explicitly instead of first-match dispatch silently dropping actions.
--install-from returns as a hidden tombstone that errors with the
replacement instead of feeding the flag to the LLM as prompt text.
--list-bundles dispatches before config load so a pure read no longer
boots MCP servers. write_file_atomic fsyncs before the rename so a crash
cannot persist a truncated store. REPL: .uninstall accepts --yes,
.install rejects trailing tokens after a category, and .install remote
gets a migration hint. Plus polish: host validation rejects '#' and '?',
renamed_to no longer serializes null, derived names get a debug assert
against the validator, completions share DEFAULT_GIT_HOST, README
mentions skills.

src/config/bundles.rs

@@ -45,6 +45,7 @@ pub(crate) struct FileRecord {
 pub(crate) struct McpServerRecord {
     pub(crate) name: String,
     pub(crate) action: McpAction,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
     pub(crate) renamed_to: Option<String>,
     /// Hash of the mcp.json entry as written; a later mismatch means the user
     /// modified it. Absent on records made before entry hashing existed.
@@ -299,6 +300,10 @@ impl BundleStore {
             );
         }
 
+        debug_assert!(
+            validate_bundle_name(&resolved.name).is_ok(),
+            "derived bundle names must satisfy validate_bundle_name"
+        );
         Ok(resolved)
     }
 
@@ -391,8 +396,10 @@ impl BundleStore {
     }
 
     /// An entry whose key any bundle already owns transfers to `bundle`, and
-    /// its `replaced` action upgrades to `transferred`; plain `replaced`
-    /// marks a pre-existing user entry that uninstall must never delete.
+    /// its `replaced` action upgrades to `transferred` only when the prior
+    /// record proves bundle origin. A prior `replaced` record marks a
+    /// pre-existing user entry that uninstall must never delete, and that
+    /// marker survives re-records and cross-bundle transfers.
     pub(crate) fn record_mcp_servers(
         &mut self,
         bundle: &str,
@@ -402,14 +409,21 @@ impl BundleStore {
         for mut entry in entries {
             let key = entry.effective_key().to_string();
             let mut previously_owned = false;
+            let mut prior_user_origin = false;
             for record in self.bundles.values_mut() {
                 let before = record.mcp_servers.len();
-                record
-                    .mcp_servers
-                    .retain(|owned| owned.effective_key() != key);
+                record.mcp_servers.retain(|owned| {
+                    if owned.effective_key() != key {
+                        return true;
+                    }
+                    if owned.action == McpAction::Replaced {
+                        prior_user_origin = true;
+                    }
+                    false
+                });
                 previously_owned |= record.mcp_servers.len() != before;
             }
-            if previously_owned && entry.action == McpAction::Replaced {
+            if previously_owned && !prior_user_origin && entry.action == McpAction::Replaced {
                 entry.action = McpAction::Transferred;
             }
             self.bundles
@@ -852,6 +866,64 @@ mod tests {
         assert_eq!(servers[0].sha256.as_deref(), Some("deadbeef"));
     }
 
+    #[test]
+    fn mcp_rerecord_of_own_replaced_entry_stays_replaced() {
+        let dir = TempStoreDir::new("bundles-mcp-sticky-self");
+        let mut store = dir.store();
+        store
+            .upsert_bundle("omc", metadata("https://github.com/x/omc", "abc123"))
+            .unwrap();
+        store
+            .record_mcp_servers(
+                "omc",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        store
+            .record_mcp_servers(
+                "omc",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        assert_eq!(
+            store.get("omc").unwrap().mcp_servers[0].action,
+            McpAction::Replaced
+        );
+    }
+
+    #[test]
+    fn mcp_transfer_of_replaced_entry_keeps_user_origin_marker() {
+        let dir = TempStoreDir::new("bundles-mcp-sticky-transfer");
+        let mut store = dir.store();
+        store
+            .upsert_bundle("alpha", metadata("https://github.com/a/alpha", "abc123"))
+            .unwrap();
+        store
+            .upsert_bundle("beta", metadata("https://github.com/b/beta", "def456"))
+            .unwrap();
+        store
+            .record_mcp_servers(
+                "alpha",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        store
+            .record_mcp_servers(
+                "beta",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        assert!(store.get("alpha").unwrap().mcp_servers.is_empty());
+        assert_eq!(
+            store.get("beta").unwrap().mcp_servers[0].action,
+            McpAction::Replaced
+        );
+    }
+
     #[test]
     fn mcp_transfer_matches_renamed_entries_by_effective_key() {
         let dir = TempStoreDir::new("bundles-mcp-renamed");
@@ -893,7 +965,7 @@ mod tests {
             .unwrap();
 
         let resolved = store
-            .resolve_bundle_name("git@github.com:X/omc.git", None)
+            .resolve_bundle_name("git@github.com:x/omc.git", None)
             .unwrap();
 
         assert_eq!(resolved.name, "omc");

src/config/install_remote.rs

@@ -151,7 +151,7 @@ fn looks_like_remote_source(value: &str) -> bool {
     }
 }
 
-const DEFAULT_GIT_HOST: &str = "github.com";
+pub(crate) const DEFAULT_GIT_HOST: &str = "github.com";
 
 fn is_repo_shorthand(value: &str) -> bool {
     let path = strip_ref_suffix(value);
@@ -174,7 +174,7 @@ fn expand_repo_shorthand(value: &str, git_host: Option<&str>) -> Result<String>
         .or_else(|| raw.strip_prefix("http://"))
         .unwrap_or(raw)
         .trim_matches('/');
-    if host.is_empty() || host.contains('/') || host.chars().any(char::is_whitespace) {
+    if host.is_empty() || host.contains(['/', '#', '?']) || host.chars().any(char::is_whitespace) {
         bail!("invalid --git-host '{raw}': expected a bare host like git.somedomain.com");
     }
     Ok(format!("https://{host}/{value}"))
@@ -951,12 +951,18 @@ fn clone_to_temp(url: &str, reference: Option<&str>) -> Result<TempRepoDir> {
                 "1".into(),
                 "--branch".into(),
                 r.into(),
+                "--".into(),
                 url.into(),
                 dest_arg,
             ])?;
         }
         Some(r) => {
-            run_git(vec!["clone".into(), url.into(), dest_arg.clone()])?;
+            run_git(vec![
+                "clone".into(),
+                "--".into(),
+                url.into(),
+                dest_arg.clone(),
+            ])?;
             run_git(vec!["-C".into(), dest_arg, "checkout".into(), r.into()])?;
         }
         None => {
@@ -964,6 +970,7 @@ fn clone_to_temp(url: &str, reference: Option<&str>) -> Result<TempRepoDir> {
                 "clone".into(),
                 "--depth".into(),
                 "1".into(),
+                "--".into(),
                 url.into(),
                 dest_arg,
             ])?;
@@ -1223,14 +1230,17 @@ fn sanitize_host(host: &str) -> String {
         .to_string()
 }
 
+/// The host compares case-insensitively but the path keeps its case: many
+/// self-hosted forges treat repository paths as case-sensitive, and collapsing
+/// distinct repos into one record misdirects updates and uninstalls.
 pub(crate) fn canonical_source_url(url: &str) -> String {
     let (host, path) = split_host_and_path(url);
-    let mut path = path.to_ascii_lowercase();
-    if let Some(stripped) = path.strip_suffix(".git")
-        && !stripped.is_empty()
-        && !stripped.ends_with('/')
-    {
-        path = stripped.to_string();
+    let mut path = path;
+    if path.to_ascii_lowercase().ends_with(".git") {
+        let stripped = &path[..path.len() - 4];
+        if !stripped.is_empty() && !stripped.ends_with('/') {
+            path.truncate(path.len() - 4);
+        }
     }
     let host = host.to_ascii_lowercase();
     if host.is_empty() {
@@ -2837,10 +2847,14 @@ mod tests {
     }
 
     #[test]
-    fn canonical_source_url_lowercases_host_and_path() {
+    fn canonical_source_url_lowercases_host_but_not_path() {
         assert_eq!(
             canonical_source_url("https://GitHub.COM/X/R.git"),
-            "github.com/x/r"
+            "github.com/X/R"
+        );
+        assert_ne!(
+            canonical_source_url("https://gitlab.example.com/team/Repo"),
+            canonical_source_url("https://gitlab.example.com/team/repo")
         );
     }
 

src/config/request_context.rs

@@ -3501,7 +3501,9 @@ impl RequestContext {
                     InstallFilter::NAMES.iter().map(|s| s.to_string()).collect(),
                 );
             } else if prev == "--git-host" {
-                values = super::map_completion_values(vec!["github.com".to_string()]);
+                values = super::map_completion_values(vec![
+                    super::install_remote::DEFAULT_GIT_HOST.to_string(),
+                ]);
             } else {
                 let has_filter = args.iter().enumerate().any(|(i, a)| {
                     a.starts_with("--filter=") || (*a == "--filter" && i < args.len() - 1)