This is very basic question that I should have resolved long ago but didn't and it still plagues me.
Let $TQ$ be the tangent bundle of some (configuration) manifold, $Q$, and let $(\pmb{q},\pmb{v}) = (q^1,\dots q^n,v^1,\dots v^n):TQ\to \mathbb{R}^{2n}$ be any local natural/induced/tangent-lifted coordinates on $TQ$ (many write $v^i=\dot{q}^i$). Let $\mathbf{X}\in\mathfrak{X}(TQ)$ be a vector field and $u_t\in TQ$ some integral curve which I will regard as $u_t = ( r_t , \mathbf{u}_t ) \in [r_t] \times T_r Q$. I am confused about the left-hand-side of the equations of motion defined by
$$ \tfrac{d}{dt}u_t = \mathbf{X}_{u_t} $$
I will use $\dot{(\cdot)}=\frac{d(\cdot)}{dt}$. Lets make it specific to second order equations such that $\mathbf{X}=v^i \partial_{q^i} + F^i\partial_{v^i}$ for $F^i\in\mathcal{F}(TQ)$. For example, the Euler-Lagrange equations can be expressed as such a field:
$$ \mathbf{X} = v^i \partial_{q^i} - g^{ij}( \tfrac{\partial L}{\partial q^k \partial v^j} v^k - \tfrac{\partial L}{\partial q^j} ) \partial_{v^i} $$
The integral curves of such fields are then of the form $u_t = (r_t,\dot{r}_t)$ such that $\dot{u}_t = (\dot{r}_t, \ddot{r}_t) $. However, it is clear from every source I've encountered that, while $\dot{r}$ is just the velocity along the curve in the usual sense, $\ddot{r}$ does NOT mean as the acceleration along the curve (we need the covariant derivative for that I believe). Instead, everybody seems to imply that $\ddot{r} = \ddot{q}^i \partial_{v^i}$ and so $\dot{u}_t$ is given simply by $\dot{u} =\dot{q}^i\partial_{q^i} + \ddot{q}^i \partial_{v^i}$ (where, for short, I'm using $\dot{q}^i$ to mean $\dot{q}^i = \frac{d}{dt}(q^i\circ r_t)\equiv v^i(\dot{r})$). I have no idea why we can say this. Clearly, $\tfrac{d}{dt}$ does not mean what I am used to when it is applied to a curve on $TQ$. I am used to it simply meaning the (total) time derivative so that if $\dot{r}=\dot{q}^i\partial_{q^i}$ then I would expect $\ddot{r}=\ddot{q}^i\partial_{q^i}+ \dot{q}^i \frac{d}{dt}\partial_{q^i}$ where the second term would then involve the covariant derivative of $\partial_{q^i}$ along $r_t$. But that is not what is going on.
short version: If $u_t=(r_t,\dot{r}_t)\in TQ$ why is the derivative of this curve given by $\dot{u}_t=\dot{q}^i\partial_{q^i} + \ddot{q}^i\partial_{v^i}$ instead of involving the actual acceleration via covariant derivative. What is the actual formula I should use to express $\dot{u}_t\in T_{u_t}(TQ)$ in a coordinate basis?
Note: I am asking this question with classical mechanics being my primary concern such that $Q$ is usually embedded in some higher dimensional flat space and where $r_t\in Q$ is a curve describing the evolution of the configuration of some mechanical system. I should maybe post this in the physics SE. I never know whether to post here or there.
Edit: part of my confusion may stem from the fact that, while I'm comfortable-ish with the "position-level" coordinate basis vectors, $\partial_{q^i}$, I still don't really know what the make of the velocity-level coordinate basis vectors, $\partial_{v^i}$. I asked a question about this at this link.