diff --git a/src/config/install_remote.rs b/src/config/install_remote.rs
index a3e2f13..f29c71a 100644
--- a/src/config/install_remote.rs
+++ b/src/config/install_remote.rs
@@ -1,17 +1,44 @@
 use anyhow::{Context, Result, bail};
+use inquire::Select;
 use std::ffi::{OsStr, OsString};
 use std::fs;
 use std::path::{Path, PathBuf};
 
-use crate::config::InstallFilter;
+use crate::config::{InstallFilter, paths};
+use crate::function::Language;
 use crate::utils;
+use crate::utils::IS_STDOUT_TERMINAL;
 
 pub fn install_remote(git_url: &str, filter: Option<InstallFilter>, force: bool) -> Result<()> {
     let (url, reference) = parse_url_with_ref(git_url)?;
     let temp = clone_to_temp(&url, reference.as_deref())?;
     println!("Cloned {git_url} to {}", temp.path().display());
-    print_repo_tree(temp.path())?;
-    let _ = (force, filter);
+
+    let layout = scan_remote_layout(temp.path())?;
+    let layout = apply_filter(layout, filter);
+
+    if layout.is_empty() {
+        println!(
+            "No recognized assets found in {git_url}. Expected one or more of: \
+             agents/, roles/, macros/, functions/tools/, functions/mcp.json"
+        );
+        return Ok(());
+    }
+
+    let plan = plan_changes(&layout)?;
+
+    if !plan.files.is_empty() {
+        print_plan_summary(&plan);
+        apply_plan(&plan, force)?;
+    }
+
+    if plan.skipped_mcp_json.is_some() {
+        println!(
+            "\nNote: functions/mcp.json detected but MCP merge is not yet wired up \
+             (Step 3 of the install-remote rollout)."
+        );
+    }
+
     Ok(())
 }
 
@@ -158,32 +185,429 @@ fn run_git(args: Vec<OsString>) -> Result<()> {
     Ok(())
 }
 
-fn print_repo_tree(root: &Path) -> Result<()> {
-    println!("Repository contents ({}):", root.display());
-    print_children(root, "")
+#[derive(Default)]
+struct RemoteLayout {
+    agents: Option<PathBuf>,
+    roles: Option<PathBuf>,
+    macros: Option<PathBuf>,
+    functions_tools: Option<PathBuf>,
+    mcp_json: Option<PathBuf>,
 }
 
-fn print_children(dir: &Path, prefix: &str) -> Result<()> {
-    let mut entries: Vec<_> = fs::read_dir(dir)
-        .with_context(|| format!("failed to read {}", dir.display()))?
-        .filter_map(|e| e.ok())
-        .filter(|e| e.file_name() != OsStr::new(".git"))
-        .collect();
-    entries.sort_by_key(|e| e.file_name());
+impl RemoteLayout {
+    fn is_empty(&self) -> bool {
+        self.agents.is_none()
+            && self.roles.is_none()
+            && self.macros.is_none()
+            && self.functions_tools.is_none()
+            && self.mcp_json.is_none()
+    }
+}
 
-    let n = entries.len();
-    for (i, entry) in entries.iter().enumerate() {
-        let is_last = i == n - 1;
-        let connector = if is_last { "└── " } else { "├── " };
-        let name = entry.file_name().to_string_lossy().to_string();
-        println!("{prefix}{connector}{name}");
+fn scan_remote_layout(root: &Path) -> Result<RemoteLayout> {
+    let mut layout = RemoteLayout::default();
 
-        if entry.file_type()?.is_dir() {
-            let extension = if is_last { "    " } else { "│   " };
-            let new_prefix = format!("{prefix}{extension}");
-            print_children(&entry.path(), &new_prefix)?;
+    let agents = root.join("agents");
+    if agents.is_dir() {
+        layout.agents = Some(agents);
+    }
+    let roles = root.join("roles");
+    if roles.is_dir() {
+        layout.roles = Some(roles);
+    }
+    let macros = root.join("macros");
+    if macros.is_dir() {
+        layout.macros = Some(macros);
+    }
+    let functions = root.join("functions");
+    if functions.is_dir() {
+        let tools = functions.join("tools");
+        if tools.is_dir() {
+            layout.functions_tools = Some(tools);
+        }
+        let mcp = functions.join("mcp.json");
+        if mcp.is_file() {
+            layout.mcp_json = Some(mcp);
         }
     }
+
+    Ok(layout)
+}
+
+fn apply_filter(mut layout: RemoteLayout, filter: Option<InstallFilter>) -> RemoteLayout {
+    let Some(filter) = filter else {
+        return layout;
+    };
+    match filter {
+        InstallFilter::Agents => RemoteLayout {
+            agents: layout.agents.take(),
+            ..RemoteLayout::default()
+        },
+        InstallFilter::Roles => RemoteLayout {
+            roles: layout.roles.take(),
+            ..RemoteLayout::default()
+        },
+        InstallFilter::Macros => RemoteLayout {
+            macros: layout.macros.take(),
+            ..RemoteLayout::default()
+        },
+        InstallFilter::Functions => RemoteLayout {
+            functions_tools: layout.functions_tools.take(),
+            ..RemoteLayout::default()
+        },
+        InstallFilter::McpConfig => RemoteLayout {
+            mcp_json: layout.mcp_json.take(),
+            ..RemoteLayout::default()
+        },
+    }
+}
+
+fn walk_files(root: &Path) -> Result<Vec<PathBuf>> {
+    let mut out = Vec::new();
+    walk_files_inner(root, &mut out)?;
+    Ok(out)
+}
+
+fn walk_files_inner(dir: &Path, out: &mut Vec<PathBuf>) -> Result<()> {
+    for entry in fs::read_dir(dir).with_context(|| format!("failed to read {}", dir.display()))? {
+        let entry = entry?;
+        let file_type = entry.file_type()?;
+        let name = entry.file_name();
+
+        if file_type.is_symlink() {
+            bail!(
+                "Symlink not allowed in remote install source: {}",
+                entry.path().display()
+            );
+        }
+        if name == OsStr::new(".git") {
+            continue;
+        }
+        if name == OsStr::new("..") {
+            bail!(
+                "Path traversal '..' not allowed: {}",
+                entry.path().display()
+            );
+        }
+
+        let path = entry.path();
+        if file_type.is_dir() {
+            walk_files_inner(&path, out)?;
+        } else if file_type.is_file() {
+            out.push(path);
+        }
+    }
+    Ok(())
+}
+
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+enum TopCategory {
+    Agents,
+    Roles,
+    Macros,
+    FunctionsTools,
+}
+
+impl TopCategory {
+    fn label(&self) -> &'static str {
+        match self {
+            TopCategory::Agents => "agents",
+            TopCategory::Roles => "roles",
+            TopCategory::Macros => "macros",
+            TopCategory::FunctionsTools => "functions/tools",
+        }
+    }
+}
+
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+enum PlannedKind {
+    New,
+    Identical,
+    Conflict,
+}
+
+struct PlannedFile {
+    src: PathBuf,
+    dst: PathBuf,
+    kind: PlannedKind,
+    top_category: TopCategory,
+}
+
+struct InstallPlan {
+    files: Vec<PlannedFile>,
+    skipped_mcp_json: Option<(PathBuf, PathBuf)>,
+}
+
+fn plan_changes(layout: &RemoteLayout) -> Result<InstallPlan> {
+    let mut files = Vec::new();
+
+    if let Some(src_dir) = &layout.agents {
+        plan_dir_into(
+            src_dir,
+            &paths::agents_data_dir(),
+            TopCategory::Agents,
+            &mut files,
+        )?;
+    }
+    if let Some(src_dir) = &layout.roles {
+        plan_dir_into(src_dir, &paths::roles_dir(), TopCategory::Roles, &mut files)?;
+    }
+    if let Some(src_dir) = &layout.macros {
+        plan_dir_into(
+            src_dir,
+            &paths::macros_dir(),
+            TopCategory::Macros,
+            &mut files,
+        )?;
+    }
+    if let Some(src_dir) = &layout.functions_tools {
+        plan_dir_into(
+            src_dir,
+            &paths::functions_dir().join("tools"),
+            TopCategory::FunctionsTools,
+            &mut files,
+        )?;
+    }
+
+    let skipped_mcp_json = layout
+        .mcp_json
+        .as_ref()
+        .map(|src| (src.clone(), paths::mcp_config_file()));
+
+    Ok(InstallPlan {
+        files,
+        skipped_mcp_json,
+    })
+}
+
+fn plan_dir_into(
+    src_dir: &Path,
+    dst_dir: &Path,
+    category: TopCategory,
+    out: &mut Vec<PlannedFile>,
+) -> Result<()> {
+    for src in walk_files(src_dir)? {
+        let rel = src
+            .strip_prefix(src_dir)
+            .expect("walk_files only returns paths under src_dir");
+        let dst = dst_dir.join(rel);
+        let kind = classify_file(&src, &dst)?;
+        out.push(PlannedFile {
+            src,
+            dst,
+            kind,
+            top_category: category,
+        });
+    }
+    Ok(())
+}
+
+fn classify_file(src: &Path, dst: &Path) -> Result<PlannedKind> {
+    if !dst.exists() {
+        return Ok(PlannedKind::New);
+    }
+    if files_equal(src, dst)? {
+        Ok(PlannedKind::Identical)
+    } else {
+        Ok(PlannedKind::Conflict)
+    }
+}
+
+const LARGE_FILE_THRESHOLD: u64 = 8 * 1024 * 1024;
+
+fn files_equal(a: &Path, b: &Path) -> Result<bool> {
+    let a_meta = fs::metadata(a).with_context(|| format!("stat {}", a.display()))?;
+    let b_meta = fs::metadata(b).with_context(|| format!("stat {}", b.display()))?;
+    if a_meta.len() != b_meta.len() {
+        return Ok(false);
+    }
+    if a_meta.len() > LARGE_FILE_THRESHOLD {
+        files_equal_streaming(a, b)
+    } else {
+        let a_bytes = fs::read(a).with_context(|| format!("read {}", a.display()))?;
+        let b_bytes = fs::read(b).with_context(|| format!("read {}", b.display()))?;
+        Ok(a_bytes == b_bytes)
+    }
+}
+
+fn files_equal_streaming(a: &Path, b: &Path) -> Result<bool> {
+    use std::io::Read;
+    let mut fa = fs::File::open(a).with_context(|| format!("open {}", a.display()))?;
+    let mut fb = fs::File::open(b).with_context(|| format!("open {}", b.display()))?;
+    let mut buf_a = [0u8; 8192];
+    let mut buf_b = [0u8; 8192];
+    loop {
+        let na = fa.read(&mut buf_a)?;
+        let nb = fb.read(&mut buf_b)?;
+        if na != nb {
+            return Ok(false);
+        }
+        if na == 0 {
+            return Ok(true);
+        }
+        if buf_a[..na] != buf_b[..nb] {
+            return Ok(false);
+        }
+    }
+}
+
+fn print_plan_summary(plan: &InstallPlan) {
+    println!("Plan:");
+    for cat in [
+        TopCategory::Agents,
+        TopCategory::Roles,
+        TopCategory::Macros,
+        TopCategory::FunctionsTools,
+    ] {
+        let new_ = count_kind(plan, cat, PlannedKind::New);
+        let identical = count_kind(plan, cat, PlannedKind::Identical);
+        let conflict = count_kind(plan, cat, PlannedKind::Conflict);
+        if new_ + identical + conflict > 0 {
+            println!(
+                "  {:<16} new={new_}  identical={identical}  conflict={conflict}",
+                cat.label()
+            );
+        }
+    }
+}
+
+fn count_kind(plan: &InstallPlan, cat: TopCategory, kind: PlannedKind) -> usize {
+    plan.files
+        .iter()
+        .filter(|p| p.top_category == cat && p.kind == kind)
+        .count()
+}
+
+#[derive(Debug, Clone, Copy, PartialEq)]
+enum StickyMode {
+    None,
+    KeepAll,
+    ReplaceAll,
+}
+
+enum ConflictAction {
+    Keep,
+    Replace,
+}
+
+struct ApplyReport {
+    new_count: usize,
+    identical_count: usize,
+    replaced_count: usize,
+    kept_count: usize,
+}
+
+fn apply_plan(plan: &InstallPlan, force: bool) -> Result<ApplyReport> {
+    let mut report = ApplyReport {
+        new_count: 0,
+        identical_count: 0,
+        replaced_count: 0,
+        kept_count: 0,
+    };
+    let mut sticky = if force {
+        StickyMode::ReplaceAll
+    } else {
+        StickyMode::None
+    };
+
+    for planned in &plan.files {
+        match planned.kind {
+            PlannedKind::New => {
+                write_file(&planned.src, &planned.dst)?;
+                report.new_count += 1;
+            }
+            PlannedKind::Identical => {
+                report.identical_count += 1;
+            }
+            PlannedKind::Conflict => match resolve_conflict(planned, &mut sticky)? {
+                ConflictAction::Keep => report.kept_count += 1,
+                ConflictAction::Replace => {
+                    write_file(&planned.src, &planned.dst)?;
+                    report.replaced_count += 1;
+                }
+            },
+        }
+    }
+
+    println!(
+        "\nInstalled: {} new, {} replaced, {} kept, {} identical.",
+        report.new_count, report.replaced_count, report.kept_count, report.identical_count
+    );
+
+    Ok(report)
+}
+
+fn resolve_conflict(planned: &PlannedFile, sticky: &mut StickyMode) -> Result<ConflictAction> {
+    match *sticky {
+        StickyMode::KeepAll => return Ok(ConflictAction::Keep),
+        StickyMode::ReplaceAll => return Ok(ConflictAction::Replace),
+        StickyMode::None => {}
+    }
+
+    if !*IS_STDOUT_TERMINAL {
+        bail!(
+            "Refusing to overwrite local file {} non-interactively. \
+             Re-run with --install-force or in a terminal.",
+            planned.dst.display()
+        );
+    }
+
+    let prompt = format!(
+        "Conflict at {} (category: {})",
+        planned.dst.display(),
+        planned.top_category.label()
+    );
+    let choice = Select::new(
+        &prompt,
+        vec!["keep", "replace", "keep-all", "replace-all", "abort"],
+    )
+    .prompt()
+    .with_context(|| "failed to read conflict choice")?;
+
+    match choice {
+        "keep" => Ok(ConflictAction::Keep),
+        "replace" => Ok(ConflictAction::Replace),
+        "keep-all" => {
+            *sticky = StickyMode::KeepAll;
+            Ok(ConflictAction::Keep)
+        }
+        "replace-all" => {
+            *sticky = StickyMode::ReplaceAll;
+            Ok(ConflictAction::Replace)
+        }
+        "abort" => bail!("Aborted by user."),
+        _ => unreachable!("inquire::Select returned an unexpected option"),
+    }
+}
+
+fn write_file(src: &Path, dst: &Path) -> Result<()> {
+    if let Some(parent) = dst.parent() {
+        fs::create_dir_all(parent)
+            .with_context(|| format!("failed to create directory {}", parent.display()))?;
+    }
+    fs::copy(src, dst)
+        .with_context(|| format!("failed to copy {} to {}", src.display(), dst.display()))?;
+    set_executable_bit_if_script(dst)?;
+    Ok(())
+}
+
+#[cfg(unix)]
+fn set_executable_bit_if_script(path: &Path) -> Result<()> {
+    use std::os::unix::fs::PermissionsExt;
+
+    let Some(ext) = path.extension().and_then(OsStr::to_str) else {
+        return Ok(());
+    };
+    if Language::from_extension(ext) == Language::Unsupported {
+        return Ok(());
+    }
+    fs::set_permissions(path, fs::Permissions::from_mode(0o755))
+        .with_context(|| format!("chmod {}", path.display()))?;
+    Ok(())
+}
+
+#[cfg(not(unix))]
+fn set_executable_bit_if_script(_path: &Path) -> Result<()> {
     Ok(())
 }
 
@@ -252,4 +676,189 @@ mod tests {
         assert!(parse_url_with_ref("https://github.com/foo/bar.git#$inject").is_err());
         assert!(parse_url_with_ref("https://github.com/foo/bar.git#;rm -rf /").is_err());
     }
+
+    fn touch(p: &Path) {
+        if let Some(parent) = p.parent() {
+            fs::create_dir_all(parent).unwrap();
+        }
+        fs::write(p, b"").unwrap();
+    }
+
+    fn fresh_temp_dir(name: &str) -> PathBuf {
+        let dir = utils::temp_file(name, "");
+        fs::create_dir_all(&dir).unwrap();
+        dir
+    }
+
+    #[test]
+    fn remote_layout_is_empty_when_default() {
+        assert!(RemoteLayout::default().is_empty());
+    }
+
+    #[test]
+    fn remote_layout_is_not_empty_when_any_field_set() {
+        let l = RemoteLayout {
+            agents: Some(PathBuf::from("/x")),
+            ..RemoteLayout::default()
+        };
+        assert!(!l.is_empty());
+    }
+
+    #[test]
+    fn apply_filter_none_passes_through() {
+        let l = RemoteLayout {
+            agents: Some(PathBuf::from("a")),
+            roles: Some(PathBuf::from("r")),
+            macros: Some(PathBuf::from("m")),
+            functions_tools: Some(PathBuf::from("f")),
+            mcp_json: Some(PathBuf::from("j")),
+        };
+        let out = apply_filter(l, None);
+        assert!(out.agents.is_some() && out.roles.is_some() && out.macros.is_some());
+        assert!(out.functions_tools.is_some() && out.mcp_json.is_some());
+    }
+
+    #[test]
+    fn apply_filter_functions_keeps_only_tools_not_mcp() {
+        let l = RemoteLayout {
+            agents: Some(PathBuf::from("a")),
+            roles: None,
+            macros: None,
+            functions_tools: Some(PathBuf::from("f")),
+            mcp_json: Some(PathBuf::from("j")),
+        };
+        let out = apply_filter(l, Some(InstallFilter::Functions));
+        assert!(out.agents.is_none());
+        assert_eq!(out.functions_tools, Some(PathBuf::from("f")));
+        assert!(out.mcp_json.is_none());
+    }
+
+    #[test]
+    fn apply_filter_mcp_config_keeps_only_mcp_json() {
+        let l = RemoteLayout {
+            agents: Some(PathBuf::from("a")),
+            roles: None,
+            macros: None,
+            functions_tools: Some(PathBuf::from("f")),
+            mcp_json: Some(PathBuf::from("j")),
+        };
+        let out = apply_filter(l, Some(InstallFilter::McpConfig));
+        assert!(out.agents.is_none() && out.functions_tools.is_none());
+        assert_eq!(out.mcp_json, Some(PathBuf::from("j")));
+    }
+
+    #[test]
+    fn apply_filter_roles_keeps_only_roles() {
+        let l = RemoteLayout {
+            agents: Some(PathBuf::from("a")),
+            roles: Some(PathBuf::from("r")),
+            macros: Some(PathBuf::from("m")),
+            functions_tools: Some(PathBuf::from("f")),
+            mcp_json: Some(PathBuf::from("j")),
+        };
+        let out = apply_filter(l, Some(InstallFilter::Roles));
+        assert_eq!(out.roles, Some(PathBuf::from("r")));
+        assert!(out.agents.is_none() && out.macros.is_none());
+        assert!(out.functions_tools.is_none() && out.mcp_json.is_none());
+    }
+
+    #[test]
+    fn walk_files_skips_dot_git_and_collects_regular_files() {
+        let root = fresh_temp_dir("walk-test-");
+        touch(&root.join("a.txt"));
+        touch(&root.join("sub/b.txt"));
+        touch(&root.join(".git/HEAD"));
+        touch(&root.join(".git/objects/pack/foo"));
+
+        let mut files = walk_files(&root).unwrap();
+        files.sort();
+        let rels: Vec<_> = files
+            .iter()
+            .map(|p| p.strip_prefix(&root).unwrap().to_owned())
+            .collect();
+
+        assert_eq!(
+            rels,
+            vec![PathBuf::from("a.txt"), PathBuf::from("sub/b.txt")]
+        );
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn walk_files_rejects_symlink() {
+        let root = fresh_temp_dir("walk-symlink-test-");
+        touch(&root.join("real.txt"));
+        std::os::unix::fs::symlink(root.join("real.txt"), root.join("link.txt")).unwrap();
+
+        let err = walk_files(&root).unwrap_err();
+        assert!(
+            err.to_string().contains("Symlink not allowed"),
+            "got error: {err}"
+        );
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn scan_remote_layout_finds_known_subdirs() {
+        let root = fresh_temp_dir("scan-test-");
+        fs::create_dir_all(root.join("agents/sample")).unwrap();
+        fs::create_dir_all(root.join("roles")).unwrap();
+        fs::create_dir_all(root.join("macros")).unwrap();
+        fs::create_dir_all(root.join("functions/tools")).unwrap();
+        touch(&root.join("functions/mcp.json"));
+        touch(&root.join("README.md"));
+
+        let layout = scan_remote_layout(&root).unwrap();
+        assert!(layout.agents.is_some());
+        assert!(layout.roles.is_some());
+        assert!(layout.macros.is_some());
+        assert!(layout.functions_tools.is_some());
+        assert!(layout.mcp_json.is_some());
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn scan_remote_layout_ignores_unrelated_files() {
+        let root = fresh_temp_dir("scan-unrelated-");
+        fs::create_dir_all(root.join("docs")).unwrap();
+        touch(&root.join("docs/intro.md"));
+        touch(&root.join("README.md"));
+
+        let layout = scan_remote_layout(&root).unwrap();
+        assert!(layout.is_empty());
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn classify_file_new_when_dst_missing() {
+        let dir = fresh_temp_dir("classify-new-");
+        let src = dir.join("src");
+        fs::write(&src, b"hello").unwrap();
+        let dst = dir.join("dst");
+        assert_eq!(classify_file(&src, &dst).unwrap(), PlannedKind::New);
+        let _ = fs::remove_dir_all(&dir);
+    }
+
+    #[test]
+    fn classify_file_identical_when_bytes_match() {
+        let dir = fresh_temp_dir("classify-identical-");
+        let src = dir.join("src");
+        let dst = dir.join("dst");
+        fs::write(&src, b"same bytes").unwrap();
+        fs::write(&dst, b"same bytes").unwrap();
+        assert_eq!(classify_file(&src, &dst).unwrap(), PlannedKind::Identical);
+        let _ = fs::remove_dir_all(&dir);
+    }
+
+    #[test]
+    fn classify_file_conflict_when_bytes_differ() {
+        let dir = fresh_temp_dir("classify-conflict-");
+        let src = dir.join("src");
+        let dst = dir.join("dst");
+        fs::write(&src, b"version A").unwrap();
+        fs::write(&dst, b"version B").unwrap();
+        assert_eq!(classify_file(&src, &dst).unwrap(), PlannedKind::Conflict);
+        let _ = fs::remove_dir_all(&dir);
+    }
 }
diff --git a/src/function/mod.rs b/src/function/mod.rs
index 0fab009..e9d0ec4 100644
--- a/src/function/mod.rs
+++ b/src/function/mod.rs
@@ -60,7 +60,13 @@ pub enum Language {
 
 impl From<&String> for Language {
     fn from(s: &String) -> Self {
-        match s.to_lowercase().as_str() {
+        Language::from_extension(s)
+    }
+}
+
+impl Language {
+    pub fn from_extension(ext: &str) -> Self {
+        match ext.to_lowercase().as_str() {
             "sh" => Language::Bash,
             "py" => Language::Python,
             "ts" => Language::TypeScript,