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Suppose that $Y$ is a connected (nonempty) topological 1-manifold without boundary; let $y$ be a point. As observed in comments, the complement $Y - \{y\}$ has two open connected components $U$ and $V$, and $Y$ can be reconstructed by gluing together $U \cup \{y\}$ and $V \cup \{y\}$, which are 1-manifolds with one boundary point each.

Suppose a subset $D \subset X$ (which we will assume is closed) is well-ordered under the order it inherits from $X$. The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

We can now classify the possibilities for $X$, according to the smallest ordinal $\xi$ which does not occur as a well-ordered subset of $X$. This dictates what well-ordered subsets $D$ that are cofinal in $X$ look like.

• If $\xi = \omega_1 + 1$, then any well-ordered cofinal $D$ must be of type $\omega_1$, and $X$ is a topological union (a directed colimit) of open sets $[0, d)$ where $d$ ranges over $D$. This union is homeomorphic to a long half-open ray.

• If $\xi = \omega_1$, then any well-ordered cofinal $D$ is countable. This forces $X$ to be homeomorphic to $\mathbb{R}_{\geq 0}$.

Suppose that $Y$ is a connected (nonempty) topological 1-manifold without boundary; let $y$ be a point. Unless $Y$ is a circle, the complement $Y - \{y\}$ has two open connected components $U$ and $V$, and $Y$ can be reconstructed by gluing together $U \cup \{y\}$ and $V \cup \{y\}$, which are 1-manifolds with one boundary point each.

Suppose a closed subset $D \subset X$ is well-ordered under the order it inherits from $X$. The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

We can now classify the possibilities for $X$, according to the smallest ordinal $\xi$ which does not occur as a well-ordered closed subset of $X$. This dictates what well-ordered closed subsets $D$ that are cofinal in $X$ look like.

• If $\xi = \omega_1 + 1$, then any closed well-ordered cofinal $D$ must be of type $\omega_1$, and $X$ is a topological union (a directed colimit) of open sets $[0, d)$ where $d$ ranges over $D$. This union is homeomorphic to a long half-open ray.

• If $\xi = \omega_1$, then any closed well-ordered cofinal $D$ is countable. This forces $X$ to be homeomorphic to $\mathbb{R}_{\geq 0}$.

Suppose a subset $D \subset X$ is well-ordered under the order it inherits from $X$. The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

Suppose a subset $D \subset X$ (which we will assume is closed) is well-ordered under the order it inherits from $X$. The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

Suppose a closed set $D \subset X$ is discretely embedded in $X$ (meaning that under the subspace topology, it is discrete). Then $D$ is in fact well-ordered under the order it inherits from $X$. For if $S \subseteq D$ is any nonempty subset, say with a point $s$, then $[0, s] \cap S$ is both compact and discrete, therefore finite and totally ordered, hence it possesses a minimal element which is minimal in $S$.

  The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

We can now classify the possibilities for $X$, according to the smallest ordinal $\xi$ which cannot be discretely embedded in $X$. This dictates what closed discrete subsets $D$ that are cofinal in $X$ look like.

• If $\xi = \omega_1 + 1$, then any cofinal discrete closed subset $D$ must be of type $\omega_1$, and $X$ is a topological union (a directed colimit) of open sets $[0, d)$ where $d$ ranges over $D$. This union is homeomorphic to a long half-open ray.

• If $\xi = \omega_1$, then any cofinal discrete closed $D$ is countable. This forces $X$ to be homeomorphic to $\mathbb{R}_{\geq 0}$.

Suppose a subset $D \subset X$ is well-ordered under the order it inherits from $X$. The order type of such $D$ must be $\omega_1$ (the first uncountable ordinal) or less. For otherwise, there would be an initial segment $S$ of $D$ of order type $\omega_1 + 1$. In that case, if $s$ is the top element of $S$, the interval $[0, s)$, which is homeomorphic to $\mathbb{R}_{\geq 0}$, would contain $\omega_1$ as a suborder -- but this is absurd since $\mathbb{R}_{\geq 0}$ has a countable cofinal set.

We can now classify the possibilities for $X$, according to the smallest ordinal $\xi$ which does not occur as a well-ordered subset of $X$. This dictates what well-ordered subsets $D$ that are cofinal in $X$ look like.

• If $\xi = \omega_1 + 1$, then any well-ordered cofinal $D$ must be of type $\omega_1$, and $X$ is a topological union (a directed colimit) of open sets $[0, d)$ where $d$ ranges over $D$. This union is homeomorphic to a long half-open ray.

• If $\xi = \omega_1$, then any well-ordered cofinal $D$ is countable. This forces $X$ to be homeomorphic to $\mathbb{R}_{\geq 0}$.